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1

The Genographic Project Public Participation Mitochondrial DNA Database  

Microsoft Academic Search

The Genographic Project is studying the genetic signatures of ancient human migrations and creating an open-source research database. It allows members of the public to participate in a real-time anthropological genetics study by submitting personal samples for analysis and donating the genetic results to the database. We report our experience from the first 18 months of public participation in the

Doron M Behar; Saharon Rosset; Jason Blue-Smith; Oleg Balanovsky; Shay Tzur; David Comas; R. John Mitchell; Lluis Quintana-Murci; Chris Tyler-Smith; R. Spencer Wells

2007-01-01

2

“A Faustian bargain?” Public voices on forensic DNA technologies and the National DNA Database  

Microsoft Academic Search

This article draws on the idea of the “forensic imaginary” (Williams 2010) to explore UK public perspectives on the place, role and significance of forensic DNA technologies, both independent of and in relation to other genetic applications. Using correspondents’ replies to the Spring 2006 Mass Observation Directive “Genes, Genetics and Cloning,” the analysis focuses on continuities and tensions in their

Dana Wilson-Kovacs; David Wyatt; Christine Hauskeller

2012-01-01

3

On the reliability of DNA sequences of Ophiocordyceps sinensis in public databases.  

PubMed

Some DNA sequences in the International Nucleotide Sequence Databases (INSD) are erroneously annotated, which has lead to misleading conclusions in publications. Ophiocordyceps sinensis (syn. Cordyceps sinensis) is a fungus endemic to the Tibetan Plateau, and more than 100 populations covering almost its distribution area have been examined by us over recent years. In this study, using the data from authentic materials, we have evaluated the reliability of nucleotide sequences annotated as O. sinensis in the INSD. As of October 15, 2012, the INSD contained 874 records annotated as O. sinensis, including 555 records representing nuclear ribosomal DNA (63.5 %), 197 representing protein-coding genes (22.5 %), 92 representing random markers with unknown functions (10.5 %), and 30 representing microsatellite loci (3.5 %). Our analysis indicated that 39 of the 397 internal transcribed spacer entries, 27 of the 105 small subunit entries, and five of the 53 large subunit entries were incorrectly annotated as belonging to O. sinensis. For protein-coding sequences, all records of serine protease genes, the mating-type gene MAT1-2-1, the DNA lyase gene, the two largest subunits of RNA polymerase II, and elongation factor-1? gene were correct, while 14 of the 73 ?-tubulin entries were indeterminate. Genetic diversity analyses using those sequences correctly identified as O. sinensis revealed significant genetic differentiation in the fungus although the extent of genetic differentiation varied with the gene. The relationship between O. sinensis and some other related fungal taxa is also discussed. PMID:23397071

Zhang, Shu; Zhang, Yong-Jie; Liu, Xing-Zhong; Zhang, Hong; Liu, Dian-Sheng

2013-02-09

4

The National DNA Database  

Microsoft Academic Search

Over the last two years the Forensic Science Service (FSS) has developed and put into operation a National DNA Database that has analysed samples from individuals suspected of crime and stains from scenes of crime. It has provided more than 2200 links between individuals and scenes and 1200 links between scenes of crime. It uses an STR SGM (second generation

David J Werrett

1997-01-01

5

A well placed trust?: Public perceptions of the governance of DNA databases  

Microsoft Academic Search

Biobanks that are run on an opt-in basis depend on people having the motivation to give and to trust in those who control their samples. Yet in the UK trust in the healthcare system has been in decline and there have been a number of health-related scandals that have received widespread media and public attention. Given this background, and the

Mairi Levitt; Sue Weldon

2005-01-01

6

An annotated mtDNA database  

Microsoft Academic Search

We have compiled a database of mitochondrial DNA (mtDNA) control region, hypervariable regions 1 (HVR1) and 2 (HVR2) sequences\\u000a of a total of 14,138 individuals compiled from 103 mtDNA publications before 1 January 2000, 13 data sets published in 2000\\u000a and 2001 and 2 unpublished data sets of Iraqi Kurds and Indians from Kerala. By contacting the authors and by

Arne Röhl; Bernd Brinkmann; Lucy Forster; P. Forster

2001-01-01

7

AIDS PUBLIC INFORMATION DATABASE  

EPA Science Inventory

The AIDS Public Information Data Set is computer software designed to run on a Microsoft Windows microcomputer, and contains information abstracted from acquired immunodeficiency syndrome (AIDS) cases reported in the United States. The data set is created by the Division of HIV/A...

8

Developing a DNA variant database.  

PubMed

Disease- and locus-specific variant databases have been a valuable resource to clinical and research geneticists. With the recent rapid developments in technologies, the number of DNA variants detected in a typical molecular genetics laboratory easily exceeds 1,000. To keep track of the growing inventory of DNA variants, many laboratories employ information technology to store the data as well as distributing the data and its associated information to clinicians and researchers via the Web. While it is a valuable resource, the hosting of a web-accessible database requires collaboration between bioinformaticians and biologists and careful planning to ensure its usability and availability. In this chapter, a series of tutorials on building a local DNA variant database out of a sample dataset will be provided. However, this tutorial will not include programming details on building a web interface and on constructing the web application necessary for web hosting. Instead, an introduction to the two commonly used methods for hosting web-accessible variant databases will be described. Apart from the tutorials, this chapter will also consider the resources and planning required for making a variant database project successful. PMID:18453092

Fung, David C Y

2008-01-01

9

Database Support for Research in Public Administration  

ERIC Educational Resources Information Center

|This study examines the extent to which databases support student and faculty research in the area of public administration. A list of journals in public administration, public policy, political science, public budgeting and finance, and other related areas was compared to the journal content list of six business databases. These databases

Tucker, James Cory

2005-01-01

10

Compressing DNA sequence databases with coil  

PubMed Central

Background Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems. Currently, sequence data is usually kept in large "flat files," which are then compressed using standard Lempel-Ziv (gzip) compression – an approach which rarely achieves good compression ratios. While much research has been done on compressing individual DNA sequences, surprisingly little has focused on the compression of entire databases of such sequences. In this study we introduce the sequence database compression software coil. Results We have designed and implemented a portable software package, coil, for compressing and decompressing DNA sequence databases based on the idea of edit-tree coding. coil is geared towards achieving high compression ratios at the expense of execution time and memory usage during compression – the compression time represents a "one-off investment" whose cost is quickly amortised if the resulting compressed file is transmitted many times. Decompression requires little memory and is extremely fast. We demonstrate a 5% improvement in compression ratio over state-of-the-art general-purpose compression tools for a large GenBank database file containing Expressed Sequence Tag (EST) data. Finally, coil can efficiently encode incremental additions to a sequence database. Conclusion coil presents a compelling alternative to conventional compression of flat files for the storage and distribution of DNA sequence databases having a narrow distribution of sequence lengths, such as EST data. Increasing compression levels for databases having a wide distribution of sequence lengths is a direction for future work.

White, W Timothy J; Hendy, Michael D

2008-01-01

11

Publications of Australian LIS Academics in Databases  

ERIC Educational Resources Information Center

|This paper examines aspects of journal articles published from 1967 to 2008, located in eight databases, and authored or co-authored by academics serving for at least two years in Australian LIS programs from 1959 to 2008. These aspects are: inclusion of publications in databases, publications in journals, authorship characteristics of…

Wilson, Concepcion S.; Boell, Sebastian K.; Kennan, Mary Anne; Willard, Patricia

2011-01-01

12

DSSTox Public Database Network Glossary of Terms  

EPA Pesticide Factsheets

CRD:  (Chemical Relational Database) A Chemical Relational Database (CRD) application is a specialized relational database application that imports and exports standard format SDF files, and that includes both a graphical chemical structure field in addition to data and text fields. CRDs generally have chemically intelligent structure-searching functions that allow a user to search records using generalized structure queries (e.g., based on atoms, atom and bond type, structural fragments, etc.) in addition to searching across data and text fields. DSSTox does not provide an on-line CRD capability for searching DSSTox SDF files, but provides information on a variety of commercial and public CRD application options available to users. More on CRDs (http://www.epa.gov/ncct/dsstox/MoreonCRDs.html)   From DSSTox Public Database Network Glossary of Terms  -  Search all glossaries for terms containing ((what is) intelligence)

2013-07-09

13

REPAIRtoire--a database of DNA repair pathways.  

PubMed

REPAIRtoire is the first comprehensive database resource for systems biology of DNA damage and repair. The database collects and organizes the following types of information: (i) DNA damage linked to environmental mutagenic and cytotoxic agents, (ii) pathways comprising individual processes and enzymatic reactions involved in the removal of damage, (iii) proteins participating in DNA repair and (iv) diseases correlated with mutations in genes encoding DNA repair proteins. REPAIRtoire provides also links to publications and external databases. REPAIRtoire contains information about eight main DNA damage checkpoint, repair and tolerance pathways: DNA damage signaling, direct reversal repair, base excision repair, nucleotide excision repair, mismatch repair, homologous recombination repair, nonhomologous end-joining and translesion synthesis. The pathway/protein dataset is currently limited to three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The DNA repair and tolerance pathways are represented as graphs and in tabular form with descriptions of each repair step and corresponding proteins, and individual entries are cross-referenced to supporting literature and primary databases. REPAIRtoire can be queried by the name of pathway, protein, enzymatic complex, damage and disease. In addition, a tool for drawing custom DNA-protein complexes is available online. REPAIRtoire is freely available and can be accessed at http://repairtoire.genesilico.pl/. PMID:21051355

Milanowska, Kaja; Krwawicz, Joanna; Papaj, Grzegorz; Kosinski, Jan; Poleszak, Katarzyna; Lesiak, Justyna; Osinska, Ewelina; Rother, Kristian; Bujnicki, Janusz M

2010-11-04

14

IRSS Public Opinion Poll Question Database  

NSDL National Science Digital Library

This database, constructed by the Institute for Research in Social Science (IRSS) at the University of North Carolina at Chapel Hill, allows researchers to conduct keyword searches on questions derived from a collection of public opinion polls, dating from the 1960s to the present. Query results display the full text of the poll questions, information about the studies, and, in many searches, frequency distributions. Users also have the option to view the full catalog record and download data from selected studies from the data archive. The IRSS Public Opinion Poll Question Database is an excellent resource for researchers who are developing "questions for their own studies, as well as for users interested in frequencies or in locating particular variables for statistical analysis."

15

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2010 CFR

...2010-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2010-04-01

16

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2010 CFR

...2009-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2009-04-01

17

24 CFR 81.72 - Public-use database and public information.  

Code of Federal Regulations, 2013 CFR

...2013-04-01 false Public-use database and public information. 81.72 ...Information § 81.72 Public-use database and public information. (a) General...available for public use, a public-use database containing public data as defined...

2013-04-01

18

Angiosperm DNA C-Values Database  

NSDL National Science Digital Library

The 1992 Global Convention on Biological Diversity (Rio de Janeiro) specified the need to make biodiversity data available "despite imperfections, rather than holding back information until more polished products are completed." Few organizations have done so. This Royal Botanic Gardens (Kew, UK) genome biodiversity database is one valuable exception. Founded in 1759, the Royal Botanic Gardens, Kew has built its unique collections which now include 6 million dried plant specimens - covering 90% of the world's plant species; 40,000 living plant taxa - estimated as 10% of the world's flora; and 80,000 fungi and artifacts of plant origin. Known best among botanists as a global resource for definitively identifying, classifying, and naming plants and fungi, Kew also maintains this database on DNA C-values. To access this free, searchable database, the user must provide an email address as well as the genus of interest; search results include Taxon, Family, 4C DNA amount (pg), and entry number/reference citation, listed separately for each species.

1997-01-01

19

76 FR 1137 - Publicly Available Consumer Product Safety Information Database: Notice of Public Web Conferences  

Federal Register 2010, 2011, 2012, 2013

...Information Database: Notice of Public Web Conferences AGENCY: Consumer Product Safety...or ``we'') is announcing two Web conferences to demonstrate to interested...information database (``Database''). The Web conferences will be webcast live from...

2011-01-07

20

Exploration of the Chemical Space of Public Genomic Databases  

EPA Science Inventory

The current project aims to chemically index the content of public genomic databases to make these data accessible in relation to other publicly available, chemically-indexed toxicological information. ...

21

MICA: desktop software for comprehensive searching of DNA databases  

PubMed Central

Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software.

Stokes, William A; Glick, Benjamin S

2006-01-01

22

Forensic utilization of familial searches in DNA databases.  

PubMed

DNA evidence is widely recognized as an invaluable tool in the process of investigation and identification, as well as one of the most sought after types of evidence for presentation to a jury. In the United States, the development of state and federal DNA databases has greatly impacted the forensic community by creating an efficient, searchable system that can be used to eliminate or include suspects in an investigation based on matching DNA profiles - the profile already in the database to the profile of the unknown sample in evidence. Recent changes in legislation have begun to allow for the possibility to expand the parameters of DNA database searches, taking into account the possibility of familial searches. This article discusses prospective positive outcomes of utilizing familial DNA searches and acknowledges potential negative outcomes, thereby presenting both sides of this very complicated, rapidly evolving situation. PMID:20739248

Gershaw, Cassandra J; Schweighardt, Andrew J; Rourke, Linda C; Wallace, Margaret M

2010-08-23

23

PAQ database: Stockholm Public Health Questionnaire  

Cancer.gov

Stockholm Public Health Questionnaire In: Leijon O, Wiktorin C, Harenstam A, Karlqvist L; MOA Research Group. Validity of a self-administered questionnaire for assessing physical work loads in a general population. J Occup Environ Med 2002 Aug;44(8):724-35.

24

Digital Equipment Corporation's CRDOM Software and Database Publications.  

ERIC Educational Resources Information Center

Acquaints information professionals with Digital Equipment Corporation's compact optical disk read-only-memory (CDROM) search and retrieval software and growing library of CDROM database publications (COMPENDEX, Chemical Abstracts Services). Highlights include MicroBASIS, boolean operators, range operators, word and phrase searching, proximity…

Adams, Michael Q.

1986-01-01

25

Biological Databases at DNA Data Bank of Japan in the Era of Next-Generation Sequencing Technologies  

Microsoft Academic Search

\\u000a The Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) has operated biological databases since 1987 in collaboration\\u000a with NCBI and EBI. As one of the three major public databases, CIB-DDBJ has run four primary databases DDBJ, CIBEX, DDBJ Trace\\u000a Archive (DTA), and DDBJ Read Archive (DRA) to collect, archive, and provide various kinds of biological data. As

Yuichi Kodama; Eli Kaminuma; Satoshi Saruhashi; Kazuho Ikeo; Hideaki Sugawara; Yoshio Tateno; Yasukazu Nakamura

26

Protein identification in DNA databases by peptide mass fingerprinting.  

PubMed Central

Proteins can be identified using a set of peptide fragment weights produced by a specific digestion to search a protein database in which sequences have been replaced by fragment weights calculated for various cleavage methods. We present a method using multidimensional searches that greatly increases the confidence level for identification, allowing DNA sequence databases to be examined. This method provides a link between 2-dimensional gel electrophoresis protein databases and genome sequencing projects. Moreover, the increased confidence level allows unknown proteins to be matched to expressed sequence tags, potentially eliminating the need to obtain sequence information for cloning. Database searching from a mass profile is offered as a free service by an automatic server at the ETH, Zürich. For information, send an electronic message to the address cbrg/inf.ethz.ch with the line: help mass search, or help all.

James, P.; Quadroni, M.; Carafoli, E.; Gonnet, G.

1994-01-01

27

Construction of a primary DNA fingerprint database for cotton cultivars.  

PubMed

Forty core primers were used to construct a DNA fingerprint database of 132 cotton species based on multiplex fluorescence detection technology. A high first successful ratio of 99.04% was demonstrated with tetraplex polymerase chain reaction. Forty primer pairs amplified a total of 262 genotypes among 132 species, with an average of 6.55 per primer and values of polymorphism information content varying from 0.340 to 0.882. Conflicting DNA homozygous ratios were found in various species. The highest DNA homozygous ratio was found in landrace standard cultivars, which had an 81.46% DNA homozygous ratio. The lowest occurred in a group of 2010 leading cultivars with a homozygous ratio of 63.04%. Genetic diversity of the 132 species was briefly analyzed using unweighted pair-group method with arithmetic means. PMID:23408447

Zhang, Y C; Kuang, M; Yang, W H; Xu, H X; Zhou, D Y; Wang, Y Q; Feng, X A; Su, C; Wang, F

2013-06-13

28

Forensic DNA Sampling and the England and Wales National DNA Database: A Sceptical Approach  

Microsoft Academic Search

This paper explores possible implications of the rapid expansion of the England and Wales National DNA Database (NDNAD), and\\u000a the current DNA sampling of offenders and the retention of samples. A precis of the justifications enunciated for the NDNAD\\u000a is followed by a sceptic's rebuttal and wider analysis of the impact of the growth of forensic DNA testing. It is

Carole Mccartney

2004-01-01

29

A study of Spanish attitudes regarding the custody and use of forensic DNA databases.  

PubMed

One of the issues that has resulted in much disagreement in many countries at different levels concerns the kind of institution that should be given the responsibility of exercising custody over biological samples and the DNA profiles obtained from these samples. In the field of forensic genetics, there is no doubt that the existence of DNA criminal databases benefits the control and investigation of crime. However, certain criticism, supported to a great extent by the particular vision of genetic exceptionalism has been aimed at the ethical and social consequences resulting from the inappropriate use of such databases. In this sense, it was stated that the support of the population was required for those regulations that propose the extension of police powers in the collection and storage of biological samples, as well as their corresponding DNA analyses. Without such backing, such measures may cause society to distrust the nature of the protection afforded by the legal system and be interpreted as interference in the civil liberties and human rights of the individual. We believe that the opinion poll which has been carried out among the Spanish population may serve to reveal the public attitudes/criteria which society has with regard to those institutions responsible for the custody of DNA profile databases. Finally, it must be pointed out that when the interviewees were asked about what institution or institutions should protect and maintain data confidentiality 59.7% considered that custody should remain in the hands of the National Agency for DNA Profiles (a judicially backed, autonomous public institution). PMID:19083809

Gamero, Joaquín-Jose; Romero, José-Luis; Peralta, Juan-Luis; Corte-Real, Francisco; Guillén, Margarita; Anjos, Maria-Joao

2008-03-01

30

A distributed system for DNA/protein database similarity searches.  

PubMed

A distributed system for exhaustive alignment similarity searches on DNA/protein databases is presented. The system makes it possible to share the computational burden on diverse computers, provided they are interconnected by a network supporting TCP/IP communication. It consists of three separate programs: a user-interface module, a similarity score calculation module (multiple instances of which may be running simultaneously on different machines), and a control module. This last acts as the 'hub' of the system. The three programs have been successfully tested under the AIX, SunOS, VAX/VMS and MS/DOS operating systems. PMID:7922683

Penotti, F E

1994-06-01

31

DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS TO DATABASES FOR BUILDING STRUCTURE-TOXICITY PREDICTION MODELS  

EPA Science Inventory

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction Models Ann M. Richard US Environmental Protection Agency, Research Triangle Park, NC, USA Distributed: Decentralized set of standardized, field-delimited databases,...

32

Avoiding the “usual suspects”: young people's views of the National DNA Database  

Microsoft Academic Search

The aim of this project was to explore the views of young people, in particular those whose details are held on the National DNA Database (NDNAD), about some of the social and ethical issues surrounding the NDNAD. Ten focus groups revealed the majority of participants supported a universal DNA database; many thought taking a DNA sample should depend on the

R. Stackhouse; C. Anderson; A. M. Shaw; R. Iredale

2010-01-01

33

TabSQL: a MySQL tool to facilitate mapping user data to public databases  

PubMed Central

Background With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. Results We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. Conclusions TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.

2010-01-01

34

Forensic DNA databases in England and the Netherlands: governance, structure and performance compared  

Microsoft Academic Search

How do liberal democracies govern forensic DNA databasing? That is the question being asked in this contribution by focusing on the rules for inclusion of samples\\/profiles in DNA databases in England and Wales and the Netherlands. The two different modes of governance shall be evaluated by taking into account models and ideas in each society regarding the two imperatives of

Victor Toom

2012-01-01

35

Development and expansion of high-quality control region databases to improve forensic mtDNA evidence interpretation.  

PubMed

In an effort to increase the quantity, breadth and availability of mtDNA databases suitable for forensic comparisons, we have developed a high-throughput process to generate approximately 5000 control region sequences per year from regional US populations, global populations from which the current US population is derived and global populations currently under-represented in available forensic databases. The system utilizes robotic instrumentation for all laboratory steps from pre-extraction through sequence detection, and a rigorous eight-step, multi-laboratory data review process with entirely electronic data transfer. Over the past 3 years, nearly 10,000 control region sequences have been generated using this approach. These data are being made publicly available and should further address the need for consistent, high-quality mtDNA databases for forensic testing. PMID:19083747

Irwin, Jodi A; Saunier, Jessica L; Strouss, Katharine M; Sturk, Kimberly A; Diegoli, Toni M; Just, Rebecca S; Coble, Michael D; Parson, Walther; Parsons, Thomas J

2007-03-13

36

MitBASE : a comprehensive and integrated mitochondrial DNA database. The present status  

Microsoft Academic Search

MitBASE is an integrated and comprehensive database of mitochondrial DNA data which collects, under a single interface, databases for Plant, Vertebrate, Invertebrate, Human, Protist and Fungal mtDNA and a Pilot database on nuclear genes involved in mito- chondrial biogenesis in Saccharomyces cerevisiae. MitBASE reports all available information from different organisms and from intraspecies variants and mutants. Data have been drawn

Marcella Attimonelli; N. Altamatura; R. Benne; A. Brennicke; J. M. Cooper; Domenica D'elia; A. De Montalvo; B. De Pinto; Mariateresa De Robertis; P. Golik; V. Knoop; Cecilia Lanave; Jaga Lazowska; Flavio Licciulli; B. S. Malladi; F. Memeo; M. Monnerot; R. Pasimeni; Sandrine Pilbout; A. H. V. Schapira; P. Sloof; Cecilia Saccone

2000-01-01

37

Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase  

PubMed Central

Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.

2009-01-01

38

High-throughput STR analysis for DNA database using direct PCR.  

PubMed

Since the Korean criminal DNA database was launched in 2010, we have focused on establishing an automated DNA database profiling system that analyzes short tandem repeat loci in a high-throughput and cost-effective manner. We established a DNA database profiling system without DNA purification using a direct PCR buffer system. The quality of direct PCR procedures was compared with that of conventional PCR system under their respective optimized conditions. The results revealed not only perfect concordance but also an excellent PCR success rate, good electropherogram quality, and an optimal intra/inter-loci peak height ratio. In particular, the proportion of DNA extraction required due to direct PCR failure could be minimized to <3%. In conclusion, the newly developed direct PCR system can be adopted for automated DNA database profiling systems to replace or supplement conventional PCR system in a time- and cost-saving manner. PMID:23683293

Sim, Jeong Eun; Park, Su Jeong; Lee, Han Chul; Kim, Se-Yong; Kim, Jong Yeol; Lee, Seung Hwan

2013-05-17

39

STRBase: a short tandem repeat DNA database for the human identity testing community  

Microsoft Academic Search

The National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http:\\/\\/www.cstl.nist.gov\\/ biotech\\/strbase\\/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase consolidates and organizes the abundant literature on this

Christian M. Ruitberg; Dennis J. Reeder; John M. Butler

2001-01-01

40

CD-ROM REVIEW: The ICRP Database of Dose Coefficients: Workers and Members of the Public  

Microsoft Academic Search

This CD contains the ICRP database of dose coefficients for workers and members of the public prepared by the DOCAL Task Group of ICRP Committee 2, and adopted by the Commission in October 1998. It is essentially an electronic version of ICRP Publications 68 and 72 for workers and members of the public, respectively. However, it contains far more data

Alan Bunker

1999-01-01

41

From Relationships to Relationship Marketing: Applying Database Technology to Public Relations.  

ERIC Educational Resources Information Center

|Notes that advances in new technologies and uses of databases have expanded the definition of publics and increased the ability to target messages to narrower and narrower ranges of publics. Explores the implications of these developments for the public relations profession. (RS)|

Petrison, Lisa A.; Wang, Paul

1993-01-01

42

Evaluating DNA profile evidence when the suspect is identified through a database search  

Microsoft Academic Search

ABSTRACT: The paper is concerned with the strength of DNA evidence when a suspect is identified via a search through a database of the DNA profiles of known,individuals. Consideration of the appropriate likelihood ratio shows that in this setting the DNA evidence is (slightly) stronger than when,a suspect is identified by other means, subsequently profiled, and found to match. The

Dj Balding; P Donnelly

1996-01-01

43

An agent- and ontology-based system for integrating public gene, protein, and disease databases.  

PubMed

In this paper, we describe OntoFusion, a database integration system. This system has been designed to provide unified access to multiple, heterogeneous biological and medical data sources that are publicly available over Internet. Many of these databases do not offer a direct connection, and inquiries must be made via Web forms, returning results as HTML pages. A special module in the OntoFusion system is needed to integrate these public 'Web-based' databases. Domain ontologies are used to do this and provide database mapping and unification. We have used the system to integrate seven significant and widely used public biomedical databases: OMIM, PubMed, Enzyme, Prosite and Prosite documentation, PDB, SNP, and InterPro. A case study is detailed in depth, showing system performance. We analyze the system's architecture and methods and discuss its use as a tool for biomedical researchers. PMID:16621723

Alonso-Calvo, R; Maojo, V; Billhardt, H; Martin-Sanchez, F; García-Remesal, M; Pérez-Rey, D

2006-03-20

44

DOE's Public Database for Green Building Case Studies: Preprint  

SciTech Connect

To help capture valuable information on''green building'' case studies, the U.S. Department of Energy has created an online database for collecting, standardizing, and disseminating information about high-performance, green projects. Type of information collected includes green features, design processes, energy performance, and comparison to other high-performance, green buildings.

Torcellini, P. A.; Crawley, D. B.

2003-11-01

45

Forensic DNA databases in Western Balkan region: retrospectives, perspectives, and initiatives  

PubMed Central

The European Network of Forensic Science Institutes (ENFSI) recommended the establishment of forensic DNA databases and specific implementation and management legislations for all EU/ENFSI members. Therefore, forensic institutions from Bosnia and Herzegovina, Serbia, Montenegro, and Macedonia launched a wide set of activities to support these recommendations. To assess the current state, a regional expert team completed detailed screening and investigation of the existing forensic DNA data repositories and associated legislation in these countries. The scope also included relevant concurrent projects and a wide spectrum of different activities in relation to forensics DNA use. The state of forensic DNA analysis was also determined in the neighboring Slovenia and Croatia, which already have functional national DNA databases. There is a need for a ‘regional supplement’ to the current documentation and standards pertaining to forensic application of DNA databases, which should include regional-specific preliminary aims and recommendations.

Marjanovic, Damir; Konjhodzic, Rijad; Butorac, Sara Sanela; Drobnic, Katja; Merkas, Sinisa; Lauc, Gordan; Primorac, Damir; An?elinovic, Simun; Milosavljevic, Mladen; Karan, Zeljko; Vidovic, Stojko; Stojkovic, Oliver; Panic, Bojana; Vucetic Dragovic, An?elka; Kovacevic, Sandra; Jakovski, Zlatko; Asplen, Chris; Primorac, Dragan

2011-01-01

46

Forensic DNA databases in Western Balkan region: retrospectives, perspectives, and initiatives.  

PubMed

The European Network of Forensic Science Institutes (ENFSI) recommended the establishment of forensic DNA databases and specific implementation and management legislations for all EU/ENFSI members. Therefore, forensic institutions from Bosnia and Herzegovina, Serbia, Montenegro, and Macedonia launched a wide set of activities to support these recommendations. To assess the current state, a regional expert team completed detailed screening and investigation of the existing forensic DNA data repositories and associated legislation in these countries. The scope also included relevant concurrent projects and a wide spectrum of different activities in relation to forensics DNA use. The state of forensic DNA analysis was also determined in the neighboring Slovenia and Croatia, which already have functional national DNA databases. There is a need for a 'regional supplement' to the current documentation and standards pertaining to forensic application of DNA databases, which should include regional-specific preliminary aims and recommendations. PMID:21674821

Marjanovi?, Damir; Konjhodzi?, Rijad; Butorac, Sara Sanela; Drobnic, Katja; Merkas, Sinisa; Lauc, Gordan; Primorac, Damir; Andjelinovi?, Simun; Milosavljevi?, Mladen; Karan, Zeljko; Vidovi?, Stojko; Stojkovi?, Oliver; Pani?, Bojana; Vuceti? Dragovi?, Andjelka; Kovacevi?, Sandra; Jakovski, Zlatko; Asplen, Chris; Primorac, Dragan

2011-06-01

47

A New Passenger Support System for Public Transport using Mobile Database Access  

Microsoft Academic Search

We have been developing a mobile passenger support system for public transport. Passen- gers can make their travel plans and purchase necessary tickets by accessing databases via the system. After starting the travel, a mo- bile terminal checks the travel schedule of its user by accessing several databases and gath- ering various kinds of information. In this ap- plication field,

Koichi Goto; Yahiko Kambayashi

2002-01-01

48

Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds  

Microsoft Academic Search

ABSTRACT: BACKGROUND: Since 2004 public cheminformatic databases and their collective functionality for exploring relationships between compounds, protein sequences, literature and assay data have advanced dramatically. In parallel, commercial sources that extract and curate such relationships from journals and patents have also been expanding. This work updates a previous comparative study of databases chosen because of their bioactive content, availability of

Christopher Southan; P'eter V'arkonyi; Sorel Muresan

2009-01-01

49

Proposals to Regulate the Public's Rights to Use Information Stored in Databases  

NSDL National Science Digital Library

One of the items on the agenda for the 1996 World Intellectual Property Organization (WIPO) Diplomatic Conference (December 2-20 1996), is a database treaty that would effect the way databases are treated in terms of intellectual property. The proposed treaty "seeks to safeguard makers of databases against misappropriation of the fruits of their financial and professional investment in collecting, verifying and presenting the contents of databases. It does this by proposing protection that covers the whole or substantial parts of a database against certain acts by a user or by a competitor, for the limited duration of the right." Some have interpreted this to mean that the facts in the databases will become the intellectual property of the creators of the databases, a development that will have important consequences. Interested Internauts can decide for themselves by reading the treaty and a selection of responses that have been posted at public-domain.org.

1996-01-01

50

Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database  

PubMed Central

Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L.) genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5%) within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5%) was the most abundant followed by AAG (12.1%), AAT (10.9%), and AT (10.3%).The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.

2012-01-01

51

Databases and Bioinformatics Tools for the Study of DNA Repair  

PubMed Central

DNA is continuously exposed to many different damaging agents such as environmental chemicals, UV light, ionizing radiation, and reactive cellular metabolites. DNA lesions can result in different phenotypical consequences ranging from a number of diseases, including cancer, to cellular malfunction, cell death, or aging. To counteract the deleterious effects of DNA damage, cells have developed various repair systems, including biochemical pathways responsible for the removal of single-strand lesions such as base excision repair (BER) and nucleotide excision repair (NER) or specialized polymerases temporarily taking over lesion-arrested DNA polymerases during the S phase in translesion synthesis (TLS). There are also other mechanisms of DNA repair such as homologous recombination repair (HRR), nonhomologous end-joining repair (NHEJ), or DNA damage response system (DDR). This paper reviews bioinformatics resources specialized in disseminating information about DNA repair pathways, proteins involved in repair mechanisms, damaging agents, and DNA lesions.

Milanowska, Kaja; Rother, Kristian; Bujnicki, Janusz M.

2011-01-01

52

The EDNAP mitochondrial DNA population database (EMPOP) collaborative exercises: organisation, results and perspectives  

Microsoft Academic Search

This paper presents an overview of the organisation and the results of the collaborative exercises (CE) of the European DNA Profiling (EDNAP) Group’s mitochondrial DNA population database project (EMPOP). The aim of the collaborative exercises was to determine whether uniformity of mtDNA sequencing results could be achieved among different laboratories. These were asked to sequence either the complete mtDNA control

Walther Parson; Anita Brandstätter; Antonio Alonso; Nathalie Brandt; Bernd Brinkmann; Angel Carracedo; Daniel Corach; Olivier Froment; Ivana Furac; Tomasz Grzybowski; Karin Hedberg; Christine Keyser-Tracqui; Tomasz Kupiec; Sabine Lutz-Bonengel; Bente Mevag; Rafal Ploski; Hermann Schmitter; Peter Schneider; Denise Syndercombe-Court; Eric Sørensen; Heather Thew; Gillian Tully; Richard Scheithauer

2004-01-01

53

[Current status of DNA databases in the forensic field: new progress, new legal needs].  

PubMed

One of the most polemic issues regarding the use of deoxyribonucleic acid (DNA) in the legal sphere, refers to the creation of DNA databases. Until relatively recently, Spain did not have a law to support the establishment of a national DNA profile bank for forensic purposes, and preserve the fundamental rights of subjects whose data are archived therein. The regulatory law of police databases regarding identifiers obtained from DNA approved in 2007, covers this void in the Spanish legislation and responds to the incessant need to adapt the laws to continuous scientific and technological progress. PMID:20476694

Baeta, Miriam; Martínez-Jarreta, Begoña

54

Update of MmtDB: a Metazoa mitochondrial DNA variants database  

Microsoft Academic Search

The present paper describes the improvements in MmtDB, a specialised database designed to collect Metazoa mitochondrial DNA variants. Priority in the data collection has been given to Metazoa for which a large amount of variants is available, e.g., for humans. Starting from the sequences available in the Nucleo- tide Sequence Databases, the redundant sequences have been removed and new sequences

Marcella Attimonelli; D. Calo; A. De Montalvo; Cecilia Lanave; D. Sasanelli; M. Tommaseo Ponzetta; Cecilia Saccone

1998-01-01

55

Complementarity between public and commercial databases: new opportunities in medicinal chemistry informatics  

Microsoft Academic Search

The last two years have seen a dramatic expansion in public cheminformatics, as exemplified by the approximate five-fold growth of PubChem from over 50 contributing data sources. Consequently, medicinal chemists who were hitherto limited to commercial databases now also have access to public sources that they can download and\\/or query directly over the Web. The range of public sources, particularly

Christopher Southan; P'eter V'arkonyi; Sorel Muresan

2007-01-01

56

A new database of mitochondrial DNA hypervariable regions I and II sequences from 162 Japanese individuals  

Microsoft Academic Search

A database of mitochondrial DNA (mtDNA) hypervariable region 1 (HV1) and region 2 (HV2) sequences of the mtDNA control region\\u000a was established from 162 unrelated Japanese individuals. The random match probability and the genetic diversity for this database\\u000a were 0.96% and 0.997, respectively. Length heteroplasmy in the C-stretch regions located around position 16189 in HV1 and\\u000a 310 in HV2 was

K. Imaizumi; T. J. Parsons; M. Yoshino; M. M. Holland

2002-01-01

57

Supporting Public Browsing of an Art Gallery Collections Database  

Microsoft Academic Search

Increased public awareness and usage of the Web suggests that a commensurate Web presence is required from providers of cultural\\u000a heritage information such as Galleries and Museums. While galleries have traditionally supplied goal-driven search facilities\\u000a to specialists, they must now provide browsing and query facilities to casual users, with less precise information seeking\\u000a requirements. Hypertext systems provide an appropriate technology

Sean Bechhofer; Nick Drummond; Carole A. Goble

2000-01-01

58

Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database  

Microsoft Academic Search

Large forensic mtDNA databases which adhere to strict guidelines for generation and maintenance, are not available for many populations outside of the United States and western Europe. We have established a high quality mtDNA control region sequence database for urban Nairobi as both a reference database for forensic investigations, and as a tool to examine the genetic variation of Kenyan

Anita Brandstätter; Christine T. Peterson; Jodi A. Irwin; Solomon Mpoke; Davy K. Koech; Walther Parson; Thomas J. Parsons

2004-01-01

59

Looking for Cancer Clues in Publicly Accessible Databases  

PubMed Central

What started out as a mere attempt to tentatively identify proteins in experimental cancer-related 2D-PAGE maps developed into VIRTUAL2D, a web-accessible repository for theoretical pI/MW charts for 92 organisms. Using publicly available expression data, we developed a collection of tissue-specific plots based on differential gene expression between normal and diseased states. We use this comparative cancer proteomics knowledge base, known as the tissue molecular anatomy project (TMAP), to uncover threads of cancer markers common to several types of cancer and to relate this information to established biological pathways.

Lemkin, Peter F.; Smythers, Gary W.; Munroe, David J.

2004-01-01

60

The annotation and the usage of scientific databases could be improved with public issue tracker software  

PubMed Central

Since the publication of their longtime predecessor The Atlas of Protein Sequences and Structures in 1965 by Margaret Dayhoff, scientific databases have become a key factor in the organization of modern science. All the information and knowledge described in the novel scientific literature is translated into entries in many different scientific databases, making it possible to obtain very accurate information on a biological entity like genes or proteins without having to manually review the literature on it. However, even for the databases with the finest annotation procedures, errors or unclear parts sometimes appear in the publicly released version and influence the research of unaware scientists using them. The researcher that finds an error in a database is often left in a uncertain state, and often abandons the effort of reporting it because of a lack of a standard procedure to do so. In the present work, we propose that the simple adoption of a public error tracker application, as in many open software projects, could improve the quality of the annotations in many databases and encourage feedback from the scientific community on the data annotated publicly. In order to illustrate the situation, we describe a series of errors that we found and helped solve on the genes of a very well-known pathway in various biomedically relevant databases. We would like to show that, even if a majority of the most important scientific databases have procedures for reporting errors, these are usually not publicly visible, making the process of reporting errors time consuming and not useful. Also, the effort made by the user that reports the error often goes unacknowledged, putting him in a discouraging position.

Dall'Olio, Giovanni Marco; Bertranpetit, Jaume; Laayouni, Hafid

2010-01-01

61

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies  

PubMed Central

Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%–63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with “overprediction” of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.

Schnoes, Alexandra M.; Brown, Shoshana D.; Dodevski, Igor; Babbitt, Patricia C.

2009-01-01

62

Molecular scaffold analysis of natural products databases in the public domain.  

PubMed

Natural products represent important sources of bioactive compounds in drug discovery efforts. In this work, we compiled five natural products databases available in the public domain and performed a comprehensive chemoinformatic analysis focused on the content and diversity of the scaffolds with an overview of the diversity based on molecular fingerprints. The natural products databases were compared with each other and with a set of molecules obtained from in-house combinatorial libraries, and with a general screening commercial library. It was found that publicly available natural products databases have different scaffold diversity. In contrast to the common concept that larger libraries have the largest scaffold diversity, the largest natural products collection analyzed in this work was not the most diverse. The general screening library showed, overall, the highest scaffold diversity. However, considering the most frequent scaffolds, the general reference library was the least diverse. In general, natural products databases in the public domain showed low molecule overlap. In addition to benzene and acyclic compounds, flavones, coumarins, and flavanones were identified as the most frequent molecular scaffolds across the different natural products collections. The results of this work have direct implications in the computational and experimental screening of natural product databases for drug discovery. PMID:22863071

Yongye, Austin B; Waddell, Jacob; Medina-Franco, José L

2012-08-31

63

An improved FORTRAN 77 recombinant DNA database management system with graphic extensions in GKS.  

PubMed

We have improved an existing clone database management system written in FORTRAN 77 and adapted it to our software environment. Improvements are that the database can be interrogated for any type of information, not just keywords. Also, recombinant DNA constructions can be represented in a simplified 'shorthand', whereafter a program assembles the full nucleotide sequence from the contributing fragments, which may be obtained from nucleotide sequence databases. Another improvement is the replacement of the database manager by programs, running in batch to maintain the databank and verify its consistency automatically. Finally, graphic extensions are written in Graphical Kernel System, to draw linear and circular restriction maps of recombinants. Besides restriction sites, recombinant features can be presented from the feature lines of recombinant database entries, or from the feature tables of nucleotide databases. The clone database management system is fully integrated into the sequence analysis software package from the Pasteur Institute, Paris, and is made accessible through the same menu. As a result, recombinant DNA sequences can directly be analysed by the sequence analysis programs. PMID:3450368

Van Rompuy, L L; Lesage, C; Vanderhaegen, M E; Telemans, M P; Zabeau, M F

1986-12-01

64

STANDARDIZATION AND STRUCTURAL ANNOTATION OF PUBLIC TOXICITY DATABASES: IMPROVING SAR CAPABILITIES AND LINKAGE TO 'OMICS DATA  

EPA Science Inventory

Standardization and structural annotation of public toxicity databases: Improving SAR capabilities and linkage to 'omics data Ann M. Richard', ClarLynda Williams', Jamie Burch2 'Nat Health & Environ Res Lab, US EPA, RTP, NC 27711; 2EPA/NC Central Univ Student COOP Trainee...

65

HEDS - EPA DATABASE SYSTEM FOR PUBLIC ACCESS TO HUMAN EXPOSURE DATA  

EPA Science Inventory

Human Exposure Database System (HEDS) is an Internet-based system developed to provide public access to human-exposure-related data from studies conducted by EPA's National Exposure Research Laboratory (NERL). HEDS was designed to work with the EPA Office of Research and Devel...

66

Harp: a distributed query system for legacy public libraries and structured databases  

Microsoft Academic Search

The main purpose of a digital library is to facilitate users easy access to enormous amount of globally networked information. Typically, this information includes preexisting public library catalog data, digitized document collections, and other databases. In this article, we describe the distributed query system of a digital library prototype system known as HARP. In the HARP project, we have designed

Ee-Peng Lim; Ying Lu

1999-01-01

67

Italian mitochondrial DNA database: results of a collaborative exercise and proficiency testing  

Microsoft Academic Search

This work is a review of a collaborative exercise on mtDNA analysis undertaken by the Italian working group (Ge.F.I.). A total\\u000a of 593 samples from 11 forensic genetic laboratories were subjected to hypervariable region (HVS-I\\/HVS-II) sequence analysis.\\u000a The raw lane data were sent to MtDNA Population Database (EMPOP) for an independent evaluation. For the inclusion of data\\u000a for the Italian

Chiara Turchi; Loredana Buscemi; Carlo Previderè; Pierangela Grignani; Anita Brandstätter; Alessandro Achilli; Walther Parson; Adriano Tagliabracci

2008-01-01

68

Standardisation of nomenclature for dog mtDNA D-loop: a prerequisite for launching a Canis familiaris database  

Microsoft Academic Search

Abstract Domestic dogs are increasingly involved, often as protagonists, in the forensic scene. Acknowledging this fact and benefiting from the accumulated experience on human mitochondrial DNA (mtDNA) analyses, we propose a standard for Canis familiaris mtDNA sequences as a prerequisite for the launching of the corresponding,database. # 2004 Elsevier Ireland Ltd. All rights reserved. Keywords: Canis familiaris; Dogs; Database; mtDNA

Lu? sa Pereira; B arbara Van Asch; Anto nio Amorim

69

Bioethical Biobanks: Three Concerns in Designing and Using Law Enforcement DNA Identification Databases  

Microsoft Academic Search

Federal and state law enforcement authorities have amassed large collections of DNA samples and the identifying profiles derived from them. These databases help to identify the guilty and to exonerate the innocent, but as the databanks grow, so do fears about civil liberties. The research reported here discusses three legal and social policy issues that have been raised in regard

D. H. Kaye

2006-01-01

70

Codon usage tabulated from international DNA sequence databases: status for the year 2000  

Microsoft Academic Search

The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and EBI. A list of the codon

Yasukazu Nakamura; Takashi Gojobori; Toshimichi Ikemura

2000-01-01

71

A Public HTLV-1 Molecular Epidemiology Database for Sequence Management and Data Mining  

PubMed Central

Background It is estimated that 15 to 20 million people are infected with the human T-cell lymphotropic virus type 1 (HTLV-1). At present, there are more than 2,000 unique HTLV-1 isolate sequences published. A central database to aggregate sequence information from a range of epidemiological aspects including HTLV-1 infections, pathogenesis, origins, and evolutionary dynamics would be useful to scientists and physicians worldwide. Described here, we have developed a database that collects and annotates sequence data and can be accessed through a user-friendly search interface. The HTLV-1 Molecular Epidemiology Database website is available at http://htlv1db.bahia.fiocruz.br/. Methodology/Principal Findings All data was obtained from publications available at GenBank or through contact with the authors. The database was developed using Apache Webserver 2.1.6 and SGBD MySQL. The webpage interfaces were developed in HTML and sever-side scripting written in PHP. The HTLV-1 Molecular Epidemiology Database is hosted on the Gonçalo Moniz/FIOCRUZ Research Center server. There are currently 2,457 registered sequences with 2,024 (82.37%) of those sequences representing unique isolates. Of these sequences, 803 (39.67%) contain information about clinical status (TSP/HAM, 17.19%; ATL, 7.41%; asymptomatic, 12.89%; other diseases, 2.17%; and no information, 60.32%). Further, 7.26% of sequences contain information on patient gender while 5.23% of sequences provide the age of the patient. Conclusions/Significance The HTLV-1 Molecular Epidemiology Database retrieves and stores annotated HTLV-1 proviral sequences from clinical, epidemiological, and geographical studies. The collected sequences and related information are now accessible on a publically available and user-friendly website. This open-access database will support clinical research and vaccine development related to viral genotype.

Libin, Pieter; Deforche, Koen; Edwards, Dustin; de Albuquerque-Junior, Antonio Eduardo; Vandamme, Anne-Mieke; Galvao-Castro, Bernardo; Alcantara, Luiz Carlos Junior

2012-01-01

72

Publication of population data of linearly inherited DNA markers in the International Journal of Legal Medicine.  

PubMed

This manuscript extends on earlier recommendations of the editor of the International Journal of Legal Medicine on short tandem repeat population data and provides details on specific criteria relevant for the analysis and publication of population studies on haploid DNA markers, i.e. Y-chromosomal polymorphisms and mitochondrial DNA. The proposed concept is based on review experience with the two forensic haploid markers databases YHRD and EMPOP, which are both endorsed by the International Society for Forensic Genetics. The intention is to provide guidance with the preparation of population studies and their results to improve the reviewing process and the quality of published data. We also suggest a minimal set of required information to be presented in the publication to increase understanding and use of the data. The outlined procedure has in part been elaborated with the editors of the journal Forensic Science International Genetics. PMID:20652581

Parson, Walther; Roewer, Lutz

2010-07-22

73

Bioethical Biobanks: Three Concerns in Designing and Using Law Enforcement DNA Identification Databases  

SciTech Connect

Federal and state law enforcement authorities have amassed large collections of DNA samples and the identifying profiles derived from them. These databases help to identify the guilty and to exonerate the innocent, but as the databanks grow, so do fears about civil liberties. The research reported here discusses three legal and social policy issues that have been raised in regard to these biobanks—the choice of loci to type for identifying individuals, the indefinite retention of DNA samples, and the use of the DNA samples or the identifying profiles for research purposes. It also considers the possible value of the databases for research into the genetics of human behavior and the ethics of using them for this purpose. It rejects the broad claim that such research is inherently unethical but proposes procedures for ensuring that the value of the proposed research justifies any psychosocial or other risks to the subjects of the research.

D.H. Kaye

2006-10-19

74

Genomics and Public Health Research: Can the State Allow Access to Genomic Databases?  

PubMed Central

Because many diseases are multifactorial disorders, the scientific progress in genomics and genetics should be taken into consideration in public health research. In this context, genomic databases will constitute an important source of information. Consequently, it is important to identify and characterize the State’s role and authority on matters related to public health, in order to verify whether it has access to such databases while engaging in public health genomic research. We first consider the evolution of the concept of public health, as well as its core functions, using a comparative approach (e.g. WHO, PAHO, CDC and the Canadian province of Quebec). Following an analysis of relevant Quebec legislation, the precautionary principle is examined as a possible avenue to justify State access to and use of genomic databases for research purposes. Finally, we consider the Influenza pandemic plans developed by WHO, Canada, and Quebec, as examples of key tools framing public health decision-making process. We observed that State powers in public health, are not, in Quebec, well adapted to the expansion of genomics research. We propose that the scope of the concept of research in public health should be clear and include the following characteristics: a commitment to the health and well-being of the population and to their determinants; the inclusion of both applied research and basic research; and, an appropriate model of governance (authorization, follow-up, consent, etc.). We also suggest that the strategic approach version of the precautionary principle could guide collective choices in these matters.

Cousineau, J; Girard, N; Monardes, C; Leroux, T; Jean, M Stanton

2012-01-01

75

DNA variant databases improve test accuracy and phenotype prediction in Alport syndrome.  

PubMed

X-linked Alport syndrome is a form of progressive renal failure caused by pathogenic variants in the COL4A5 gene. More than 700 variants have been described and a further 400 are estimated to be known to individual laboratories but are unpublished. The major genetic testing laboratories for X-linked Alport syndrome worldwide have established a Web-based database for published and unpublished COL4A5 variants ( https://grenada.lumc.nl/LOVD2/COL4A/home.php?select_db=COL4A5 ). This conforms with the recommendations of the Human Variome Project: it uses the Leiden Open Variation Database (LOVD) format, describes variants according to the human reference sequence with standardized nomenclature, indicates likely pathogenicity and associated clinical features, and credits the submitting laboratory. The database includes non-pathogenic and recurrent variants, and is linked to another COL4A5 mutation database and relevant bioinformatics sites. Access is free. Increasing the number of COL4A5 variants in the public domain helps patients, diagnostic laboratories, clinicians, and researchers. The database improves the accuracy and efficiency of genetic testing because its variants are already categorized for pathogenicity. The description of further COL4A5 variants and clinical associations will improve our ability to predict phenotype and our understanding of collagen IV biochemistry. The database for X-linked Alport syndrome represents a model for databases in other inherited renal diseases. PMID:23720012

Savige, Judy; Ars, Elisabet; Cotton, Richard G H; Crockett, David; Dagher, Hayat; Deltas, Constantinos; Ding, Jie; Flinter, Frances; Pont-Kingdon, Genevieve; Smaoui, Nizar; Torra, Roser; Storey, Helen

2013-05-30

76

MethylomeDB: a database of DNA methylation profiles of the brain.  

PubMed

MethylomeDB (http://epigenomics.columbia.edu/methylomedb/index.html) is a new database containing genome-wide brain DNA methylation profiles. DNA methylation is an important epigenetic mark in the mammalian brain. In human studies, aberrant DNA methylation alterations have been associated with various neurodevelopmental and neuropsychiatric disorders such as schizophrenia, and depression. In this database, we present methylation profiles of carefully selected non-psychiatric control, schizophrenia, and depression samples. We also include data on one mouse forebrain sample specimen to allow for cross-species comparisons. In addition to our DNA methylation data generated in-house, we have and will continue to include published DNA methylation data from other research groups with the focus on brain development and function. Users can view the methylation data at single-CpG resolution with the option of wiggle and microarray formats. They can also download methylation data for individual samples. MethylomeDB offers an important resource for research into brain function and behavior. It provides the first source of comprehensive brain methylome data, encompassing whole-genome DNA methylation profiles of human and mouse brain specimens that facilitate cross-species comparative epigenomic investigations, as well as investigations of schizophrenia and depression methylomes. PMID:22140101

Xin, Yurong; Chanrion, Benjamin; O'Donnell, Anne H; Milekic, Maria; Costa, Ramiro; Ge, Yongchao; Haghighi, Fatemeh G

2011-12-02

77

Development of a 20-locus fluorescent multiplex system as a valuable tool for national DNA database.  

PubMed

The multiplex system allows the detection of 19 autosomal short tandem repeat (STR) loci [including all Combined DNA Index System (CODIS) STR loci as well as D2S1338, D6S1043, D12S391, D19S433, Penta D and Penta E] plus the sex-determining locus Amelogenin in a single reaction, comprising all STR loci in various commercial kits used in the China national DNA database (NDNAD). Primers are designed so that the amplicons are distributed ranging from 90 base pairs (bp) to 450 bp within a five-dye fluorescent design with the fifth dye reserved for the internal size standard. With 30 cycles, 125 pg to 2 ng DNA template showed optimal profiling result, while robust profiles could also be achieved by adjusting the cycle numbers for the DNA template beyond that optimal DNA input range. Mixture studies showed that 83% and 87% of minor alleles were detected at 9:1 and 1:9 ratios, respectively. When 4 ng of degraded DNA was digested by 2-min DNase and 1 ng undegraded DNA was added to 400 ?M haematin, the complete profiles were still observed. Polymerase chain reaction (PCR)-based procedures were examined and optimized including the concentrations of primer set, magnesium and the Taq polymerase as well as volume, cycle number and annealing temperature. In addition, the system has been validated by 3000 bloodstain samples and 35 common case samples in line with the Chinese National Standards and Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. The total probability of identity (TPI) can reach to 8×10(-24), where DNA database can be improved at the level of 10 million DNA profiles or more because the number of expected match is far from one person (4×10(-10)) and can be negligible. Further, our system also demonstrates its good performance in case samples and it will be an ideal tool for forensic DNA typing and databasing with potential application. PMID:23266302

Jiang, Xianhua; Guo, Fei; Jia, Fei; Jin, Ping; Sun, Zhu

2012-12-21

78

DNA banking and DNA databanking: Legal, ethical, and public policy issues  

SciTech Connect

The purpose of this research was to provide support to enable the authors to: (1) perform legal and empirical research and critically analyze DNA banking and DNA databanking as those activities are conducted by state forensic laboratories, the military, academic researchers, and commercial enterprises; and (2) develop a broadcast quality educational videotape for viewing by the general public about DNA technology and the privacy and related issues that it raises. The grant thus had both a research and analysis component and a public education component. This report outlines the work completed under the project.

Reilly, P.R.; McEwen, J.E.; Lawyer, J.D.; Small, D.

1997-04-30

79

Database of amino acid-nucleotide contacts in contacts in DNA-homeodomain protein  

NASA Astrophysics Data System (ADS)

The analysis of amino acid-nucleotide contacts in interfaces of the protein-DNA complexes, intended to find consistencies in the protein-DNA recognition, is a complex problem that requires an analysis of the physicochemical characteristics of these contacts and the positions of the participating amino acids and nucleotides in the chains of the protein and the DNA, respectively, as well as conservatism of these contacts. Thus, those heterogeneous data should be systematized. For this purpose we have developed a database of amino acid-nucleotide contacts ANTPC (Amino acid Nucleotide Type Position Conservation) following the archetypal example of the proteins in the homeodomain family. We show that it can be used to compare and classify the interfaces of the protein-DNA complexes.

Grokhlina, T. I.; Zrelov, P. V.; Ivanov, V. V.; Polozov, R. V.; Chirgadze, Yu. N.; Sivozhelezov, V. S.

2013-09-01

80

SITVITWEB--a publicly available international multimarker database for studying Mycobacterium tuberculosis genetic diversity and molecular epidemiology.  

PubMed

Among various genotyping methods to study Mycobacterium tuberculosis complex (MTC) genotypic polymorphism, spoligotyping and mycobacterial interspersed repetitive units-variable number of DNA tandem repeats (MIRU-VNTRs) have recently gained international approval as robust, fast, and reproducible typing methods generating data in a portable format. Spoligotyping constituted the backbone of a publicly available database SpolDB4 released in 2006; nonetheless this method possesses a low discriminatory power when used alone and should be ideally used in conjunction with a second typing method such as MIRU-VNTRs for high-resolution epidemiological studies. We hereby describe a publicly available international database named SITVITWEB which incorporates such multimarker data allowing to have a global vision of MTC genetic diversity worldwide based on 62,582 clinical isolates corresponding to 153 countries of patient origin (105 countries of isolation). We report a total of 7105 spoligotype patterns (corresponding to 58,180 clinical isolates) - grouped into 2740 shared-types or spoligotype international types (SIT) containing 53,816 clinical isolates and 4364 orphan patterns. Interestingly, only 7% of the MTC isolates worldwide were orphans whereas more than half of SITed isolates (n=27,059) were restricted to only 24 most prevalent SITs. The database also contains a total of 2379 MIRU patterns (from 8161 clinical isolates) from 87 countries of patient origin (35 countries of isolation); these were grouped in 847 shared-types or MIRU international types (MIT) containing 6626 isolates and 1533 orphan patterns. Lastly, data on 5-locus exact tandem repeats (ETRs) were available on 4626 isolates from 59 countries of patient origin (22 countries of isolation); a total of 458 different VNTR patterns were observed - split into 245 shared-types or VNTR International Types (VIT) containing 4413 isolates) and 213 orphan patterns. Datamining of SITVITWEB further allowed to update rules defining MTC genotypic lineages as well to have a new insight into MTC population structure and worldwide distribution at country, sub-regional and continental levels. At evolutionary level, the data compiled may be useful to distinguish the occasional convergent evolution of genotypes versus specific evolution of sublineages essentially influenced by adaptation to the host. This database is publicly available at: http://www.pasteur-guadeloupe.fr:8081/SITVIT_ONLINE. PMID:22365971

Demay, Christophe; Liens, Benjamin; Burguière, Thomas; Hill, Véronique; Couvin, David; Millet, Julie; Mokrousov, Igor; Sola, Christophe; Zozio, Thierry; Rastogi, Nalin

2012-02-17

81

Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections ?  

PubMed Central

Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1? (EF-1?), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.

O'Donnell, Kerry; Sutton, Deanna A.; Rinaldi, Michael G.; Sarver, Brice A. J.; Balajee, S. Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C.; Robert, Vincent A. R. G.; Crous, Pedro W.; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M.

2010-01-01

82

Internet-accessible DNA sequence database for identifying fusaria from human and animal infections.  

PubMed

Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1? (EF-1?), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study. PMID:20686083

O'Donnell, Kerry; Sutton, Deanna A; Rinaldi, Michael G; Sarver, Brice A J; Balajee, S Arunmozhi; Schroers, Hans-Josef; Summerbell, Richard C; Robert, Vincent A R G; Crous, Pedro W; Zhang, Ning; Aoki, Takayuki; Jung, Kyongyong; Park, Jongsun; Lee, Yong-Hwan; Kang, Seogchan; Park, Bongsoo; Geiser, David M

2010-08-04

83

SetupX--a public study design database for metabolomic projects.  

PubMed

Metabolomic databases are useless without accurate description of the biological study design and accompanying metadata reporting on the laboratory workflow from sample preparation to data processing. Here we report on the implementation of a database system that enables investigators to detail and set up a biological experiment, and that also steers laboratory workflows by direct access to the data acquisition instrument. SetupX utilizes orthogonal biological parameters such as genotype, organ, and treatment(s) for delineating the dimensions of a study which define the number of classes under investigation. Publicly available taxonomic and ontology repositories are utilized to ensure data integrity and logic consistency of class designs. Class descriptions are subsequently employed to schedule and randomize data acquisitions, and to deploy metabolite annotations carried out by the seamlessly integrated mass spectrometry database, BinBase. Annotated result data files are housed by SetupX for downloads and queries. Currently, 39 users have generated 48 studies, some of which are made public. PMID:17990490

Scholz, Martin; Fiehn, Oliver

2007-01-01

84

Development and Evaluation of a Quality-Controlled Ribosomal Sequence Database for 16S Ribosomal DNA-Based Identification of Staphylococcus Species  

PubMed Central

To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5? end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of ?98.7% similarity for a “distinct species,” a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMérieux, Marcy I'Etoile, France) and VITEK 2 (bioMérieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants.

Becker, Karsten; Harmsen, Dag; Mellmann, Alexander; Meier, Christian; Schumann, Peter; Peters, Georg; von Eiff, Christof

2004-01-01

85

The internet brain volume database: a public resource for storage and retrieval of volumetric data.  

PubMed

Every month, numerous publications appear that include neuroanatomic volumetric observations. The current and past literature that includes volumetric measurements is vast, but variable with respect to specific species, structures, and subject characteristics (such as gender, age, pathology, etc.). In this report we introduce the Internet Brain Volume Database (IBVD), www.nitrc.org/projects/ibvd , a site devoted to facilitating access to and utilization of neuroanatomic volumetric observations as published in the literature. We review the design and functionality of the site. The IBVD is the first database dedicated to integrating, exposing and sharing brain volumetric observations across species and disease. It offers valuable functionality for quality assurance assessment of results as well as support for meta-analysis across large segments of the published literature that are obscured from traditional text-based search engines. PMID:21931990

Kennedy, David N; Hodge, Steven M; Gao, Yong; Frazier, Jean A; Haselgrove, Christian

2012-04-01

86

A comparison of adjustment methods to test the robustness of an STR DNA database comprised of 24 European populations  

Microsoft Academic Search

An aim of the European Network of Forensic Science Institutes (ENFSI) is to produce a DNA database of second generation multiplex (SGM) STR profiles that is representative of the resident cosmopolitan populations. To achieve this, data were collected from 24 different populations. All of the data were combined to form one database of 5700 profiles from which allele proportions were

Peter Gill; Lindsey Foreman; John S Buckleton; Christopher M Triggs; Heather Allen

2003-01-01

87

Feline non-repetitive mitochondrial DNA control region database for forensic evidence.  

PubMed

The domestic cat is the one of the most popular pets throughout the world. A by-product of owning, interacting with, or being in a household with a cat is the transfer of shed fur to clothing or personal objects. As trace evidence, transferred cat fur is a relatively untapped resource for forensic scientists. Both phenotypic and genotypic characteristics can be obtained from cat fur, but databases for neither aspect exist. Because cats incessantly groom, cat fur may have nucleated cells, not only in the hair bulb, but also as epithelial cells on the hair shaft deposited during the grooming process, thereby generally providing material for DNA profiling. To effectively exploit cat hair as a resource, representative databases must be established. The current study evaluates 402 bp of the mtDNA control region (CR) from 1394 cats, including cats from 25 distinct worldwide populations and 26 breeds. Eighty-three percent of the cats are represented by 12 major mitotypes. An additional 8.0% are clearly derived from the major mitotypes. Unique sequences are found in 7.5% of the cats. The overall genetic diversity for this data set is 0.8813±0.0046 with a random match probability of 11.8%. This region of the cat mtDNA has discriminatory power suitable for forensic application worldwide. PMID:20457082

Grahn, R A; Kurushima, J D; Billings, N C; Grahn, J C; Halverson, J L; Hammer, E; Ho, C K; Kun, T J; Levy, J K; Lipinski, M J; Mwenda, J M; Ozpinar, H; Schuster, R K; Shoorijeh, S J; Tarditi, C R; Waly, N E; Wictum, E J; Lyons, L A

2010-02-25

88

Reusable data in public health data-bases-problems encountered in Danish Children's Database.  

PubMed

Denmark have unique health informatics databases e.g. "The Children's Database", which since 2009 holds data on all Danish children from birth until 17 years of age. In the current set-up a number of potential sources of errors exist - both technical and human-which means that the data is flawed. This gives rise to erroneous statistics and makes the data unsuitable for research purposes. In order to make the data usable, it is necessary to develop new methods for validating the data generation process at the municipal/regional/national level. In the present ongoing research project, two research areas are combined: Public Health Informatics and Computer Science, and both ethnographic as well as system engineering research methods are used. The project is expected to generate new generic methods and knowledge about electronic data collection and transmission in different social contexts and by different social groups and thus to be of international importance, since this is sparsely documented in the Public Health Informatics perspective. This paper presents the preliminary results, which indicate that health information technology used ought to be subject for redesign, where a thorough insight into the work practices should be point of departure. PMID:22874263

Høstgaard, Anna Marie; Pape-Haugaard, Louise

2012-01-01

89

DNAReplication: a database of information and resources for the eukaryotic DNA replication community.  

PubMed

DNAReplication (at http://www.dnareplication.net) has been set up as a freely available single resource to facilitate access to information on eukaryotic DNA replication. This database summarizes organism-sorted data on replication proteins in the categories of nomenclature, biochemical properties, motifs, interactions, modifications, structure, cell localization and expression, and general comments. Replication concepts are defined and a general model of the steps in DNA replication is presented. Links to relevant websites and homepages of replication labs are provided. The site also has an interactive section where links to recent replication papers are posted and readers are provided with the facility to post comments about each paper. The interactive and links pages are modified weekly and the whole site is updated annually. PMID:18931374

Cotterill, Sue; Kearsey, Stephen E

2008-10-17

90

Exaggerated status of "novel" and "pathogenic" mtDNA sequence variants due to inadequate database searches.  

PubMed

Given its relative ease, screening the entire mitochondrial DNA (mtDNA) for heteroplasmic or novel homoplasmic mutations has become part of the routine diagnostic workup for the molecular geneticist confronted with a disease case exhibiting clinical and biochemical features of mitochondrial dysfunction. "Novelty" of a given mtDNA variant is most often equated with nonregistration in the extensive MITOMAP database (www.mitomap.org). This practice has led to a number of spurious findings and wrong conclusions concerning the pathogenic status of specific mtDNA mutations, especially in the absence of proper evaluation and pathogenicity scoring. We demonstrate by way of real cases targeting the mt-tRNA(Cys) (MT-TC) gene and a stretch within the MT-ND3 gene, that a straightforward Google search can identify twice as many previously observed mutations than any MITOMAP query could achieve. Further, we reassess the recent rediscovery of m.15287T>C by listing all known occurrences and, where possible, providing the haplogroup context, shedding new light on the potential pathogenicity status of m.15287T>C. PMID:18800376

Bandelt, Hans-Jürgen; Salas, Antonio; Taylor, Robert W; Yao, Yong-Gang

2009-02-01

91

EDGEdb: a transcription factor-DNA Interaction database for the analysis of C. elegans differential gene expression  

PubMed Central

Background Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome biology is to map protein-DNA interaction networks of all regulatory regions in a genome of interest. Both transcription factor -and gene-centered methods can be used to systematically identify such interactions. We use high-throughput yeast one-hybrid assays as a gene-centered method to identify protein-DNA interactions between regulatory sequences (e.g. gene promoters) and transcription factors in the nematode Caenorhabditis elegans. We have already mapped several hundred protein-DNA interactions and analyzed the transcriptional consequences of some by examining differential gene expression of targets in the presence or absence of an upstream regulator. The rapidly increasing amount of protein-DNA interaction data at a genome scale requires a database that facilitates efficient data storage, retrieval and integration. Description Here, we report the implementation of a C. elegans differential gene expression database (EDGEdb). This database enables the storage and retrieval of protein-DNA interactions and other data that relate to differential gene expression. Specifically, EDGEdb contains: i) sequence information of regulatory elements, including gene promoters, ii) sequence information of all 934 predicted transcription factors, their DNA binding domains, and, where available, their dimerization partners and consensus DNA binding sites, iii) protein-DNA interactions between regulatory elements and transcription factors, and iv) expression patterns conferred by regulatory elements, and how such patterns are affected by interacting transcription factors. Conclusion EDGEdb provides a protein-DNA -and protein-protein interaction resource for C. elegans transcription factors and a framework for similar databases for other organisms. The database is available at .

Barrasa, M Inmaculada; Vaglio, Philippe; Cavasino, Fabien; Jacotot, Laurent; Walhout, Albertha JM

2007-01-01

92

Italian mitochondrial DNA database: results of a collaborative exercise and proficiency testing.  

PubMed

This work is a review of a collaborative exercise on mtDNA analysis undertaken by the Italian working group (Ge.F.I.). A total of 593 samples from 11 forensic genetic laboratories were subjected to hypervariable region (HVS-I/HVS-II) sequence analysis. The raw lane data were sent to MtDNA Population Database (EMPOP) for an independent evaluation. For the inclusion of data for the Italian database, quality assurance procedures were applied to the control region profiles. Only eight laboratories with a final population sample of 395 subjects passed the quality conformance test. Control region haplogroup (hg) assignments were confirmed by restriction fragment length polymorphism (RFLP) typing of the most common European hg-diagnostic sites. A total of 306 unique haplotypes derived from the combined analysis of control and coding region polymorphisms were found; the most common haplotype--CRS, 263, 309.1C, 315.1C/ not7025 AluI--was shared by 20 subjects. The majority of mtDNAs detected in the Italian population fell into the most common west Eurasian hgs: R0a (0.76%), HV (4.81%), H (38.99%), HV0 (3.55%), J (7.85%), T (13.42%), U (11.65%), K (10.13%), I (1.52%), X (2.78%), and W (1.01%). PMID:17952451

Turchi, Chiara; Buscemi, Loredana; Previderè, Carlo; Grignani, Pierangela; Brandstätter, Anita; Achilli, Alessandro; Parson, Walther; Tagliabracci, Adriano

2007-10-20

93

POLLUX: a program for simulated cloning, mutagenesis and database searching of DNA constructs.  

PubMed

Computer support for research in biotechnology has developed rapidly and has provided several tools to aid the researcher. This report describes the capabilities of new computer software developed in this laboratory to aid in the documentation and planning of experiments in molecular biology. The program, POLLUX, provides a graphical medium for the entry, edit and manipulation of DNA constructs and a textual format for display and edit of construct descriptive data. Program operation and procedures are designed to mimic the actual laboratory experiments with respect to capability and the order in which they are performed. Flexible control over the content of the computer-generated displays and program facilities is provided by a mouse-driven menu interface. Programmed facilities for mutagenesis, simulated cloning and searching of the database from networked workstations are described. PMID:2059840

Dayringer, H E; Sammons, S A

1991-04-01

94

A comparison of adjustment methods to test the robustness of an STR DNA database comprised of 24 European populations.  

PubMed

An aim of the European Network of Forensic Science Institutes (ENFSI) is to produce a DNA database of second generation multiplex (SGM) STR profiles that is representative of the resident cosmopolitan populations. To achieve this, data were collected from 24 different populations. All of the data were combined to form one database of 5700 profiles from which allele proportions were calculated. The robustness of this combined European database was tested by estimating parameter d for every DNA profile, where d=log(10)(Pm(c)/Pm(E)) Pm(c) is the match probability of the profile calculated from its cognate database and Pm(E) is the match probability of the combined European database. Overall there was a small tendency for Pm(c)>Pm(E) primarily because of sampling bias. This bias was removed by the simple expediency of applying an adjustment factor to the calculation of Pm(E). These were selected from the Balding size bias correction, the Balding and Nichols Fst correction, a minimum allele proportion (between 0.01 and 0.02), an upper bound of a 95% confidence interval (CI) and a lower bound on the genotype match probability. It was demonstrated that a single European database is a feasible proposition. A combination of different adjustment methods can be used to ensure that the result is conservative relative to the cognate database, and their effect measured by parameter d. PMID:12590058

Gill, Peter; Foreman, Lindsey; Buckleton, John S; Triggs, Christopher M; Allen, Heather

2003-01-28

95

Similarity landscapes: An improved method for scientific visualization of information from protein and DNA database searches  

SciTech Connect

This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors have used computer simulations and examination of a variety of databases to answer questions about a wide range of evolutionary questions. The authors have found that there is a clear distinction in the evolution of HIV-1 and HIV-2, with the former and more virulent virus evolving more rapidly at a functional level. The authors have discovered highly non-random patterns in the evolution of HIV-1 that can be attributed to a variety of selective pressures. In the course of examination of microsatellite DNA (short repeat regions) in microorganisms, the authors have found clear differences between prokaryotes and eukaryotes in their distribution, differences that can be tied to different selective pressures. They have developed a new method (topiary pruning) for enhancing the phylogenetic information contained in DNA sequences. Most recently, the authors have discovered effects in complex rainforest ecosystems that indicate strong frequency-dependent interactions between host species and their parasites, leading to the maintenance of ecosystem variability.

Dogget, N.; Myers, G. [Los Alamos National Lab., NM (United States); Wills, C.J. [Univ. of California, San Diego, CA (United States)

1998-12-01

96

Low template STR typing: effect of replicate number and consensus method on genotyping reliability and DNA database search results.  

PubMed

To analyze DNA samples with very low DNA concentrations, various methods have been developed that sensitize short tandem repeat (STR) typing. Sensitized DNA typing is accompanied by stochastic amplification effects, such as allele drop-outs and drop-ins. Therefore low template (LT) DNA profiles are interpreted with care. One can either try to infer the genotype by a consensus method that uses alleles confirmed in replicate analyses, or one can use a statistical model to evaluate the strength of the evidence in a direct comparison with a known DNA profile. In this study we focused on the first strategy and we show that the procedure by which the consensus profile is assembled will affect genotyping reliability. In order to gain insight in the roles of replicate number and requested level of reproducibility, we generated six independent amplifications of samples of known donors. The LT methods included both increased cycling and enhanced capillary electrophoresis (CE) injection [1]. Consensus profiles were assembled from two to six of the replications using four methods: composite (include all alleles), n-1 (include alleles detected in all but one replicate), n/2 (include alleles detected in at least half of the replicates) and 2× (include alleles detected twice). We compared the consensus DNA profiles with the DNA profile of the known donor, studied the stochastic amplification effects and examined the effect of the consensus procedure on DNA database search results. From all these analyses we conclude that the accuracy of LT DNA typing and the efficiency of database searching improve when the number of replicates is increased and the consensus method is n/2. The most functional number of replicates within this n/2 method is four (although a replicate number of three suffices for samples showing >25% of the alleles in standard STR typing). This approach was also the optimal strategy for the analysis of 2-person mixtures, although modified search strategies may be needed to retrieve the minor component in database searches. From the database searches follows the recommendation to specifically mark LT DNA profiles when entering them into the DNA database. PMID:20655289

Benschop, Corina C G; van der Beek, Cornelis P; Meiland, Hugo C; van Gorp, Ankie G M; Westen, Antoinette A; Sijen, Titia

2010-07-22

97

Contextual models of clinical publications for enhancing retrieval from full-text databases.  

PubMed

Conventional methods for retrieving information from the medical literature are imprecise and inefficient. Information retrieval systems employ unmanageable indexing vocabularies or use full-text representations that overwhelm the user with irrelevant information. This paper describes a document representation designed to improve the precision of searching in textual databases without significantly compromising recall. The representation augments simple text word representations with contextual models that reflect recurring semantic themes in clinical publications. Using this representation, a searcher may indicate both the terms of interest and the contexts in which they should occur. The contexts limit the potential interpretations of text words, and thus form the basis for more precise searching. In this paper, we discuss the shortcomings of traditional retrieval systems and describe our context-based representation. Improved retrieval performance with contextual models is illustrated by example, and a more extensive study is proposed. We present an evaluation of the contextual models as an indexing scheme, using a variation of the traditional inter-indexer consistency experiments, and we demonstrate that contextual indexing is reproducible by minimally trained physicians and medical students. PMID:8563412

Purcell, G P; Shortliffe, E H

1995-01-01

98

Generation and analysis of a 29,745 unique Expressed Sequence Tags from the Pacific oyster (Crassostrea gigas) assembled into a publicly accessible database: the GigasDatabase  

Microsoft Academic Search

BACKGROUND: Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly

Elodie Fleury; Arnaud Huvet; Christophe Lelong; Julien de Lorgeril; Viviane Boulo; Yannick Gueguen; Evelyne Bachère; Arnaud Tanguy; Dario Moraga; Caroline Fabioux; Penelope Lindeque; Jenny Shaw; Richard Reinhardt; Patrick Prunet; Grace Davey; Sylvie Lapègue; Christopher Sauvage; Charlotte Corporeau; Jeanne Moal; Frederick Gavory; Patrick Wincker; François Moreews; Christophe Klopp; Michel Mathieu; Pierre Boudry; Pascal Favrel

2009-01-01

99

MMsINC®: A New Public Large-Scale Chemoinformatics Database System  

Microsoft Academic Search

MMsINC is a free web-oriented database of commercially available compounds for virtual screening and chemoinformatic applications. MMsINC contains over 4 million non-redundant chemical compounds in 3D format. The whole database was studied in term of uniqueness, diversity, frameworks, chemical reactivity, drug-like and lead-like properties. This study shows that there are more than 175.000 frameworks in our database. There are 3.89

Marco Fanton; Matteo Floris; Gianfranco Frau; Mattia Sturlese; Joel Masciocchi; Piergiorgio Palla; Fabian Cedrati; Patricia Rodriguez-tomé; Stefano Moro

2008-01-01

100

The barley EST DNA Replication and Repair Database (bEST-DRRD) as a tool for the identification of the genes involved in DNA replication and repair  

PubMed Central

Background The high level of conservation of genes that regulate DNA replication and repair indicates that they may serve as a source of information on the origin and evolution of the species and makes them a reliable system for the identification of cross-species homologs. Studies that had been conducted to date shed light on the processes of DNA replication and repair in bacteria, yeast and mammals. However, there is still much to be learned about the process of DNA damage repair in plants. Description These studies, which were conducted mainly using bioinformatics tools, enabled the list of genes that participate in various pathways of DNA repair in Arabidopsis thaliana (L.) Heynh to be outlined; however, information regarding these mechanisms in crop plants is still very limited. A similar, functional approach is particularly difficult for a species whose complete genomic sequences are still unavailable. One of the solutions is to apply ESTs (Expressed Sequence Tags) as the basis for gene identification. For the construction of the barley EST DNA Replication and Repair Database (bEST-DRRD), presented here, the Arabidopsis nucleotide and protein sequences involved in DNA replication and repair were used to browse for and retrieve the deposited sequences, derived from four barley (Hordeum vulgare L.) sequence databases, including the “Barley Genome version 0.05” database (encompassing ca. 90% of barley coding sequences) and from two databases covering the complete genomes of two monocot models: Oryza sativa L. and Brachypodium distachyon L. in order to identify homologous genes. Sequences of the categorised Arabidopsis queries are used for browsing the repositories, which are located on the ViroBLAST platform. The bEST-DRRD is currently used in our project during the identification and validation of the barley genes involved in DNA repair. Conclusions The presented database provides information about the Arabidopsis genes involved in DNA replication and repair, their expression patterns and models of protein interactions. It was designed and established to provide an open-access tool for the identification of monocot homologs of known Arabidopsis genes that are responsible for DNA-related processes. The barley genes identified in the project are currently being analysed to validate their function.

2012-01-01

101

Background Adjustment for DNA Microarrays Using a Database of Microarray Experiments  

PubMed Central

Abstract DNA microarrays have become an indispensable technique in biomedical research. The raw measurements from microarrays undergo a number of preprocessing steps before the data are converted to the genomic level for further analysis. Background adjustment is an important step in preprocessing. Estimating background noise has been challenging because background levels vary a lot from probe to probe, yet there are limited observations on each probe. Most current methods have used the empirical Bayes approach to borrow information across probes on the same array. These approaches shrink the background estimate for either the entire sample or probes sharing similar sequence structures. In this article, we present a solution that is truly probe specific by using a database of large number of microarray experiments. Information is borrowed across samples and background noise is estimated for each probe individually. The ability to obtain probe specific background distributions allows us to extend the dynamic range of gene expression levels. We illustrate the improvement in detecting gene expression variation on two datasets: a Latin Square spike-in experiment from Affymetrix and an Estrogen Receptor experiment with biological replicates. An R package dbRMA implementing our method can be obtained from the authors.

Sui, Yunxia; Zhao, Xiaoyue; Speed, Terence P.

2009-01-01

102

Public Perceptions and Expectations of the Forensic Use of DNA: Results of a Preliminary Study  

ERIC Educational Resources Information Center

|The forensic use of Deoxyribonucleic Acid (DNA) is demonstrating significant success as a crime-solving tool. However, numerous concerns have been raised regarding the potential for DNA use to contravene cultural, ethical, and legal codes. In this article the expectations and level of knowledge of the New Zealand public of the DNA data-bank and…

Curtis, Cate

2009-01-01

103

Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems)  

SciTech Connect

Integration, re-use and meta-analysis of high content study data, typical of DNA microarray studies, can increase its scientific utility. Access to study data and design parameters would enhance the mining of data integrated across studies. However, without standards for which data to include in exchange, and common exchange formats, publication of high content data is time-consuming and often prohibitive. The MGED Society ( (www.mged.org)) was formed in response to the widespread publication of microarray data, and the recognition of the utility of data re-use for meta-analysis. The NIEHS has developed the Chemical Effects in Biological Systems (CEBS) database, which can manage and integrate study data and design from biological and biomedical studies. As community standards are developed for study data and metadata it will become increasingly straightforward to publish high content data in CEBS, where they will be available for meta-analysis. Different exchange formats for study data are being developed: Standard for Exchange of Nonclinical Data (SEND; (www.cdisc.org)); Tox-ML ( (www.Leadscope.com)) and Simple Investigation Formatted Text (SIFT) from the NIEHS. Data integration can be done at the level of conclusions about responsive genes and phenotypes, and this workflow is supported by CEBS. CEBS also integrates raw and preprocessed data within a given platform. The utility and a method for integrating data within and across DNA microarray studies is shown in an example analysis using DrugMatrix data deposited in CEBS by Iconix Pharmaceuticals.

Fostel, Jennifer M. [Global Health Sector, SRA International, Inc., LLC, Durham, North Carolina (United States)], E-mail: Fostel@niehs.nih.gov

2008-11-15

104

The ICRP database of dose coefficients: Workers and members of the public, version 1.0, an extension of ICRP publications 68 and 72  

SciTech Connect

A CDROM database that gives dose coefficients for inhalation and ingestion of over 800 radionuclides of 91 elements. Inhalation dose coefficients are provided for ten aerosol sizes from 0.001 {micro}m to 10 {micro}m AMAD. Effective dose and equivalent dose coefficients are given for ten integration periods form 1 d to 70 y. Extensive help files summarizing the biokinetic models in ICRP Reports 68 and 72 are provided. The greatest value added in this CDROM, however, is the powerful help utility. These files contain test from ICRP Publications 68 and 72, diagrams of the biokinetic models, and information concerning the database. The text of Publication 68 provides a very useful summary of the ICRP respiratory tract model. Hypertext links are provided for important definitions and tables, making the CDROM much more user-friendly than the original publication. Another help file compiles all of the most recent biokinetic models for systemic activity. This is particularly useful since some have been revised recently (e.g., cesium appears in Publication 56) while others have remained unchanged since Publication 30. Consolidating these models in a single place should relieve the problem of crosschecking to assure that the most current model is being used in a dose assessment.

Vargo, G.J.

2000-03-01

105

Privacy issues with DNA databases and retention of individuals' DNA information by law enforcement agencies: the holding of the European Court of Human Rights case S and Marper v. United Kingdom should be adapted to American Fourth Amendment jurisprudence  

Microsoft Academic Search

When law enforcement agencies collect, retain, and use individuals' DNA information in DNA databases for crime prevention purposes the presumption of innocence is reduced for those individuals. Collection and use of DNA information has benefits, greatly assisting law enforcement agencies in their criminal investigations. However, problems arise when DNA information is retained and used for individuals who have been acquitted,

Michael Lwin

2010-01-01

106

Constructing a pedestrian recognition system with a public open database, without the necessity of re-training: an experimental study  

Microsoft Academic Search

Pedestrian recognition is one of the basic elements of an active pedestrian protection system. Especially, there have been\\u000a various researches to develop vision-based pedestrian classifiers. Recently, Munder and Gavrila (IEEE Trans Pattern Anal Mach\\u000a Intell 28(11):1863–1868, 2006) opened their DaimlerChrysler (DCX) pedestrian image database and tried to provide an objective comparison between popular\\u000a features and classifiers. After their publication, objective

Ho Gi Jung; Jaihie Kim

2010-01-01

107

Allergen databases.  

PubMed

Allergies represent a significant medical and industrial problem. Molecular and clinical data on allergens are growing exponentially and in this article we have reviewed nine specialized allergen databases and identified data sources related to protein allergens contained in general purpose molecular databases. An analysis of allergens contained in public databases indicates a high level of redundancy of entries and a relatively low coverage of allergens by individual databases. From this analysis we identify current database needs for allergy research and, in particular, highlight the need for a centralized reference allergen database. PMID:14616118

Brusic, V; Millot, M; Petrovsky, N; Gendel, S M; Gigonzac, O; Stelman, S J

2003-11-01

108

Searching for first-degree familial relationships in California's offender DNA database: Validation of a likelihood ratio-based approach  

Microsoft Academic Search

A validation study was performed to measure the effectiveness of using a likelihood ratio-based approach to search for possible first-degree familial relationships (full-sibling and parent–child) by comparing an evidence autosomal short tandem repeat (STR) profile to California's ?1,000,000-profile State DNA Index System (SDIS) database. Test searches used autosomal STR and Y-STR profiles generated for 100 artificial test families. When the

Steven P. Myers; Mark D. Timken; Matthew L. Piucci; Gary A. Sims; Michael A. Greenwald; James J. Weigand; Kenneth C. Konzak; Martin R. Buoncristiani

2011-01-01

109

Public-key system using DNA as a one-way function for key distribution.  

PubMed

Novel public-key system using DNA has been developed. To solve key distribution problem, the public-key cryptography system based on the one-way function has been developed. The message-encoded DNA hidden in dummies can be restored by PCR amplification, followed by sequencing. We used these operations as a one-way function, and constituted a novel method for the key distribution based on the public-key system using DNA. We will show the way of holding a key in common just between specific two persons. PMID:15917125

Tanaka, Kazuo; Okamoto, Akimitsu; Saito, Isao

2005-02-25

110

Amerindian mitochondrial DNA haplogroups predominate in the population of Argentina: towards a first nationwide forensic mitochondrial DNA sequence database  

Microsoft Academic Search

The study presents South American mitochondrial DNA (mtDNA) data from selected north (N?=?98), central (N?=?193) and south (N?=?47) Argentinean populations. Sequence analysis of the complete mtDNA control region (CR, 16024–576) resulted in 288 unique\\u000a haplotypes ignoring C-insertions around positions 16193, 309, and 573; the additional analysis of coding region single nucleotide\\u000a polymorphisms enabled a fine classification of the described lineages.

Maria Cecilia Bobillo; Bettina Zimmermann; Andrea Sala; Gabriela Huber; Alexander Röck; Hans-Jürgen Bandelt; Daniel Corach; Walther Parson

2010-01-01

111

Distributing the ERIC Database on Compact Disc: A Case History of Private Sector Involvement in the Distribution of Public Sector Data.  

ERIC Educational Resources Information Center

|Describes the partnership between the public and private sectors in developing and marketing the ERIC database in CD-ROM format. Particular emphasis is given to the marketing research and protocols of partnership that were developed. (Author/CLB)|

Brandhorst, Ted

1987-01-01

112

Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics  

PubMed Central

We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus tshawytscha) cDNA libraries (1317 ESTs), 2 sockeye salmon (Oncorhynchus nerka) cDNA libraries (1243 ESTs), and 2 lake whitefish (Coregonus clupeaformis) cDNA libraries (1465 ESTs). The majority of these are 3? sequences, allowing discrimination between paralogs arising from a recent genome duplication in the salmonid lineage. Sequence assembly reveals 28,710 different S. salar, 8981 O. mykiss, 1085 O. tshawytscha, 520 O. nerka, and 1176 C. clupeaformis putative transcripts. We annotate the submitted portion of our EST database by molecular function. Higher- and lower-molecular-weight fractions of libraries are shown to contain distinct gene sets, and higher rates of gene discovery are associated with higher-molecular weight libraries. Pyloric caecum library group annotations indicate this organ may function in redox control and as a barrier against systemic uptake of xenobiotics. A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids.

Rise, Matthew L.; von Schalburg, Kristian R.; Brown, Gordon D.; Mawer, Melanie A.; Devlin, Robert H.; Kuipers, Nathanael; Busby, Maura; Beetz-Sargent, Marianne; Alberto, Roberto; Gibbs, A. Ross; Hunt, Peter; Shukin, Robert; Zeznik, Jeffrey A.; Nelson, Colleen; Jones, Simon R.M.; Smailus, Duane E.; Jones, Steven J.M.; Schein, Jacqueline E.; Marra, Marco A.; Butterfield, Yaron S.N.; Stott, Jeff M.; Ng, Siemon H.S.; Davidson, William S.; Koop, Ben F.

2004-01-01

113

Public-key system using DNA as a one-way function for key distribution  

Microsoft Academic Search

Novel public-key system using DNA has been developed. To solve key distribution problem, the public-key cryptography system based on the one-way function has been developed. The message-encoded DNA hidden in dummies can be restored by PCR amplification, followed by sequencing. We used these operations as a one-way function, and constituted a novel method for the key distribution based on the

Kazuo Tanaka; Akimitsu Okamoto; Isao Saito

2005-01-01

114

OriDB, the DNA replication origin database updated and extended  

PubMed Central

OriDB (http://www.oridb.org/) is a database containing collated genome-wide mapping studies of confirmed and predicted replication origin sites. The original database collated and curated Saccharomyces cerevisiae origin mapping studies. Here, we report that the OriDB database and web site have been revamped to improve user accessibility to curated data sets, to greatly increase the number of curated origin mapping studies, and to include the collation of replication origin sites in the fission yeast Schizosaccharomyces pombe. The revised database structure underlies these improvements and will facilitate further expansion in the future. The updated OriDB for S. cerevisiae is available at http://cerevisiae.oridb.org/ and for S. pombe at http://pombe.oridb.org/.

Siow, Cheuk C.; Nieduszynska, Sian R.; Muller, Carolin A.; Nieduszynski, Conrad A.

2012-01-01

115

A Human Mitochondrial Genome Database  

NSDL National Science Digital Library

The Center for Molecular Medicine at Emory University maintains this human mitochondrial genome database, which offers information on Mitochondrial DNA Function Locations and Polypeptide Assignments as well as the relevant publication references. The database is initially searchable by gene, disease, and enzyme. Users can then refine their search by function, polymorphisms, or references (author, title, journal, year, or keyword). Users can also search the references directly via an Advanced Search. An additional resource at the site is a reference guide to mitomap tables featuring searchable (by keyword) information on specific mitochondrial DNA function locations and references. An opportunity to add publications to this database is available, if users find that pertinent papers have not been cited.

Kogelnik, A. M.; Wallace, D. C.; Brown, M. D.; Navathe, S. B.; Lott, M. T.; Katdare, G. C.

1996-01-01

116

A search for obligatory paternal alleles in a DNA database to find an alleged rapist in a fatherless paternity case.  

PubMed

A sexual assault case resulted in a pregnancy, which was subsequently aborted. The alleged father of the fetus was unknown. Maternal and fetal types were obtained using the 11-locus AmpF?STR(®) SGM Plus(®) kit. The national DNA database was searched for the paternal obligatory alleles and detected two suspects who could not be excluded as father of the male fetus. Additional typing using the AmpF?STR(®) Minifiler(™) kit, containing three additional autosomal loci, was not sufficient to exclude either suspect. Subsequent typing using the PowerPlex(®) 16, containing four additional loci, and Y-Filer(™) kits resulted in excluding one suspect. Searching a database for paternal obligatory alleles can be fruitful, but is fraught with possible false positive results so that finding a match must be taken as only preliminary evidence. PMID:22390833

Barash, Mark; Reshef, Ayeleth; Voskoboinik, Lev; Zamir, Ashira; Motro, Uzi; Gafny, Ron

2012-03-05

117

Towards standards for data exchange and integration and their impact on a public database such as CEBS (Chemical Effects in Biological Systems).  

PubMed

Integration, re-use and meta-analysis of high content study data, typical of DNA microarray studies, can increase its scientific utility. Access to study data and design parameters would enhance the mining of data integrated across studies. However, without standards for which data to include in exchange, and common exchange formats, publication of high content data is time-consuming and often prohibitive. The MGED Society (www.mged.org) was formed in response to the widespread publication of microarray data, and the recognition of the utility of data re-use for meta-analysis. The NIEHS has developed the Chemical Effects in Biological Systems (CEBS) database, which can manage and integrate study data and design from biological and biomedical studies. As community standards are developed for study data and metadata it will become increasingly straightforward to publish high content data in CEBS, where they will be available for meta-analysis. Different exchange formats for study data are being developed: Standard for Exchange of Nonclinical Data (SEND; www.cdisc.org); Tox-ML (www.Leadscope.com) and Simple Investigation Formatted Text (SIFT) from the NIEHS. Data integration can be done at the level of conclusions about responsive genes and phenotypes, and this workflow is supported by CEBS. CEBS also integrates raw and preprocessed data within a given platform. The utility and a method for integrating data within and across DNA microarray studies is shown in an example analysis using DrugMatrix data deposited in CEBS by Iconix Pharmaceuticals. PMID:18680759

Fostel, Jennifer M

2008-07-02

118

Automatic detection of lung nodules in computed tomography images: training and validation of algorithms using public research databases  

NASA Astrophysics Data System (ADS)

Lung cancer is one of the main public health issues in developed countries. Lung cancer typically manifests itself as non-calcified pulmonary nodules that can be detected reading lung Computed Tomography (CT) images. To assist radiologists in reading images, researchers started, a decade ago, the development of Computer Aided Detection (CAD) methods capable of detecting lung nodules. In this work, a CAD composed of two CAD subprocedures is presented: , devoted to the identification of parenchymal nodules, and , devoted to the identification of the nodules attached to the pleura surface. Both CADs are an upgrade of two methods previously presented as Voxel Based Neural Approach CAD . The novelty of this paper consists in the massive training using the public research Lung International Database Consortium (LIDC) database and on the implementation of new features for classification with respect to the original VBNA method. Finally, the proposed CAD is blindly validated on the ANODE09 dataset. The result of the validation is a score of 0.393, which corresponds to the average sensitivity of the CAD computed at seven predefined false positive rates: 1/8, 1/4, 1/2, 1, 2, 4, and 8 FP/CT.

Camarlinghi, Niccolò

2013-09-01

119

A database of mitochondrial DNA hypervariable regions I and II sequences of individuals from Slovakia.  

PubMed

In order to identify polymorphic positions and to determine their frequencies and the frequency of haplotypes in the human mitochondrial control region, two hypervariable regions (HV1 and HV2) of the mitochondrial DNA (mtDNA) of 374 unrelated individuals from Slovakia were amplified and sequenced. Sequence comparison led to the identification of 284 mitochondrial lineages as defined by 163 variable sites. Genetic diversity (GD) was estimated at 0.997 and the probability of two randomly selected individuals from population having identical mtDNA types (random match probability, RMP) for the both regions is 0.60%. PMID:19083829

Lehocký, Ivan; Baldovic, Marian; Kádasi, Ludevít; Metspalu, Ene

2008-02-14

120

[DNA databases for criminal investigation purposes: technical aspects and ethical-legal problems].  

PubMed

Advances in DNA technology and the discovery of DNA polymorphisms have opened up the possibility of creating data bases of individuals' DNA for criminal investigation purposes. In many European countries laws are being drawn up or have been passed to regulate such data bases. In Spain theres is a need for an urgent ethical and legal debate on ther appropriateness. The article is divided into two parts. In the first, the authors discuss the technical principles underlying these data bases. In the second, they set out their legal and ethical views on regulation in Spain. PMID:15839031

Guillen Vázquez, M; Pestoni, C; Carracedo, A

121

GABI-Kat SimpleSearch: new features of the Arabidopsis thaliana T-DNA mutant database  

PubMed Central

T-DNA insertion mutants are very valuable for reverse genetics in Arabidopsis thaliana. Several projects have generated large sequence-indexed collections of T-DNA insertion lines, of which GABI-Kat is the second largest resource worldwide. User access to the collection and its Flanking Sequence Tags (FSTs) is provided by the front end SimpleSearch (http://www.GABI-Kat.de). Several significant improvements have been implemented recently. The database now relies on the TAIRv10 genome sequence and annotation dataset. All FSTs have been newly mapped using an optimized procedure that leads to improved accuracy of insertion site predictions. A fraction of the collection with weak FST yield was re-analysed by generating new FSTs. Along with newly found predictions for older sequences about 20?000 new FSTs were included in the database. Information about groups of FSTs pointing to the same insertion site that is found in several lines but is real only in a single line are included, and many problematic FST-to-line links have been corrected using new wet-lab data. SimpleSearch currently contains data from ?71?000 lines with predicted insertions covering 62.5% of the 27?206 nuclear protein coding genes, and offers insertion allele-specific data from 9545 confirmed lines that are available from the Nottingham Arabidopsis Stock Centre.

Kleinboelting, Nils; Huep, Gunnar; Kloetgen, Andreas; Viehoever, Prisca; Weisshaar, Bernd

2012-01-01

122

Searching for first-degree familial relationships in California's offender DNA database: validation of a likelihood ratio-based approach.  

PubMed

A validation study was performed to measure the effectiveness of using a likelihood ratio-based approach to search for possible first-degree familial relationships (full-sibling and parent-child) by comparing an evidence autosomal short tandem repeat (STR) profile to California's ?1,000,000-profile State DNA Index System (SDIS) database. Test searches used autosomal STR and Y-STR profiles generated for 100 artificial test families. When the test sample and the first-degree relative in the database were characterized at the 15 Identifiler(®) (Applied Biosystems(®), Foster City, CA) STR loci, the search procedure included 96% of the fathers and 72% of the full-siblings. When the relative profile was limited to the 13 Combined DNA Index System (CODIS) core loci, the search procedure included 93% of the fathers and 61% of the full-siblings. These results, combined with those of functional tests using three real families, support the effectiveness of this tool. Based upon these results, the validated approach was implemented as a key, pragmatic and demonstrably practical component of the California Department of Justice's Familial Search Program. An investigative lead created through this process recently led to an arrest in the Los Angeles Grim Sleeper serial murders. PMID:21056023

Myers, Steven P; Timken, Mark D; Piucci, Matthew L; Sims, Gary A; Greenwald, Michael A; Weigand, James J; Konzak, Kenneth C; Buoncristiani, Martin R

2010-11-05

123

Evaluation and Utilization as a Public Health Tool of a National Molecular Epidemiological Tuberculosis Outbreak Database within the United Kingdom from 1997 to 2001  

PubMed Central

The aim of this study was to develop a national model and analyze the value of a molecular epidemiological Mycobacterium tuberculosis DNA fingerprint-outbreak database. Incidents were investigated by the United Kingdom PHLS Mycobacterium Reference Unit (MRU) from June 1997 to December 2001, inclusive. A total of 124 incidents involving 972 tuberculosis cases, including 520 patient cultures from referred incidents and 452 patient cultures related to two population studies, were examined by using restriction fragment length polymorphism IS6110 fingerprinting and rapid epidemiological typing. Investigations were divided into the following three categories, reflecting different operational strategies: retrospective passive analysis, retrospective active analysis, and retrospective prospective analysis. The majority of incidents were in the retrospective passive analysis category, i.e., the individual submitting isolates has a suspicion they may be linked. Outbreaks were examined in schools, hospitals, farms, prisons, and public houses, and laboratory cross-contamination events and unusual clinical presentations were investigated. Retrospective active analysis involved a major outbreak centered on a high school. Contact tracing of a teenager with smear-positive pulmonary tuberculosis matched 14 individuals, including members of his class, and another 60 cases were identified in schools clinically and radiologically and by skin testing. Retrospective prospective analysis involved an outbreak of 94 isoniazid-resistant tuberculosis cases in London, United Kingdom, that began after cases were identified at one hospital in January 2000. Contact tracing and comparison with MRU databases indicated that the earliest matched case had occurred in 1995. Subsequently, the MRU changed to an active prospective analysis targeting linked isoniazid-monoresistant isolates for follow up. The patients were multiethnic, born mainly in the United Kingdom, and included professionals, individuals from the music industry, intravenous drug abusers, and prisoners.

Drobniewski, F. A.; Gibson, A.; Ruddy, M.; Yates, M. D.

2003-01-01

124

A curated public database for multilocus sequence typing (MLST) and analysis of Haemophilus parasuis based on an optimized typing scheme.  

PubMed

Haemophilus parasuis causes Glässer's disease and pneumonia in swine. Serotyping is often used to classify isolates but requires reagents that are costly to produce and not standardized or widely available. Sequence-based methods, such as multilocus sequence typing (MLST), offer many advantages over serotyping. An MLST scheme was previously proposed for H. parasuis but genome sequence data only recently available reveals the primers recommended, based on sequences of related bacteria, are not optimal. Here we report modifications to enhance the original method, including primer redesign to eliminate mismatches with H. parasuis sequences and to avoid regions of high sequence heterogeneity, standardization of primer T(m)s and identification of universal PCR conditions that result in robust and reproducible amplification of all targets. The modified typing method was applied to a collection of 127 isolates from North and South America, Europe and Asia. An alignment of the concatenated sequences obtained from seven target housekeeping genes identified 278 variable nucleotide sites that define 116 unique sequence types. A comparison of the original and modified methods using a subset of 86 isolates indicates little difference in overall locus diversity, discriminatory power or in the clustering of strains within Neighbor-Joining trees. Data from the optimized MLST were used to populate a newly created and publicly available H. parasuis database. An accompanying database designed to capture provenance and epidemiological information for each isolate was also created. The modified MLST scheme is highly discriminatory but more robust, reproducible and user-friendly than the original. The MLST database provides a novel resource for investigation of H. parasuis outbreaks and for tracking strain evolution. PMID:23218953

Mullins, Michael A; Register, Karen B; Brunelle, Brian W; Aragon, Virginia; Galofré-Mila, Nuria; Bayles, Darrell O; Jolley, Keith A

2012-11-20

125

Mass spectrometric base composition profiling: Implications for forensic mtDNA databasing.  

PubMed

In forensic genetics mitochondrial DNA (mtDNA) is usually analyzed by direct Sanger-type sequencing (STS). This method is known to be laborious and sometimes prone to human error. Alternative methods have been proposed that lead to faster results. Among these are methods that involve mass-spectrometry resulting in base composition profiles that are, by definition, less informative than the full nucleotide sequence. Here, we applied a highly automated electrospray ionization mass spectrometry (ESI-MS) system (PLEX-ID) to an mtDNA population study to compare its performance with respect to throughput and concordance to STS. We found that the loss of information power was relatively low compared to the gain in speed and analytical standardization. The detection of point and length heteroplasmy turned out to be roughly comparable between the technologies with some individual differences related to the processes. We confirm that ESI-MS provides a valuable platform for analyzing mtDNA variation that can also be applied in the forensic context. PMID:24054029

Eduardoff, Mayra; Huber, Gabriela; Bayer, Birgit; Schmid, Dagmar; Anslinger, Katja; Göbel, Tanja; Zimmermann, Bettina; Schneider, Peter M; Röck, Alexander W; Parson, Walther

2013-09-18

126

A brief history of the formation of DNA databases in forensic science within Europe  

Microsoft Academic Search

The introduction of DNA analysis to forensic science brought with it a number of choices for analysis, not all of which were compatible. As laboratories throughout Europe were eager to use the new technology different systems became routine in different laboratories and consequently, there was no basis for the exchange of results. A period of co-operation then started in which

Peter D. Martin; Hermann Schmitter; Peter M. Schneider

2001-01-01

127

Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II): A public-access intensive care unit database  

PubMed Central

Objective We sought to develop an intensive care unit research database applying automated techniques to aggregate high-resolution diagnostic and therapeutic data from a large, diverse population of adult intensive care unit patients. This freely available database is intended to support epidemiologic research in critical care medicine and serve as a resource to evaluate new clinical decision support and monitoring algorithms. Design Data collection and retrospective analysis. Setting All adult intensive care units (medical intensive care unit, surgical intensive care unit, cardiac care unit, cardiac surgery recovery unit) at a tertiary care hospital. Patients Adult patients admitted to intensive care units between 2001 and 2007. Interventions None. Measurements and Main Results The Multiparameter Intelligent Monitoring in Intensive Care II (MIMIC-II) database consists of 25,328 intensive care unit stays. The investigators collected detailed information about intensive care unit patient stays, including laboratory data, therapeutic intervention profiles such as vasoactive medication drip rates and ventilator settings, nursing progress notes, discharge summaries, radiology reports, provider order entry data, International Classification of Diseases, 9th Revision codes, and, for a subset of patients, high-resolution vital sign trends and waveforms. Data were automatically deidentified to comply with Health Insurance Portability and Accountability Act standards and integrated with relational database software to create electronic intensive care unit records for each patient stay. The data were made freely available in February 2010 through the Internet along with a detailed user’s guide and an assortment of data processing tools. The overall hospital mortality rate was 11.7%, which varied by critical care unit. The median intensive care unit length of stay was 2.2 days (interquartile range, 1.1–4.4 days). According to the primary International Classification of Diseases, 9th Revision codes, the following disease categories each comprised at least 5% of the case records: diseases of the circulatory system (39.1%); trauma (10.2%); diseases of the digestive system (9.7%); pulmonary diseases (9.0%); infectious diseases (7.0%); and neoplasms (6.8%). Conclusions MIMIC-II documents a diverse and very large population of intensive care unit patient stays and contains comprehensive and detailed clinical data, including physiological waveforms and minute-by-minute trends for a subset of records. It establishes a new public-access resource for critical care research, supporting a diverse range of analytic studies spanning epidemiology, clinical decision-rule development, and electronic tool development.

Saeed, Mohammed; Villarroel, Mauricio; Reisner, Andrew T.; Clifford, Gari; Lehman, Li-Wei; Moody, George; Heldt, Thomas; Kyaw, Tin H.; Moody, Benjamin; Mark, Roger G.

2011-01-01

128

Development of a DNA Microarray to Detect Antimicrobial Resistance Genes Identified in the National Center for Biotechnology Information Database  

PubMed Central

To understand the mechanisms and epidemiology of antimicrobial resistance (AR), the genetic elements responsible must be identified. Due to the myriad of possible genes, a high-density genotyping technique is needed for initial screening. To achieve this, AR genes in the National Center for Biotechnology Information GenBank database were identified by their annotations and compiled into a nonredundant list of 775 genes. A DNA microarray was constructed of 70mer oligonucelotide probes designed to detect these genes encoding resistances to aminoglycosides, ?-lactams, chloramphenicols, glycopeptides, heavy metals, lincosamides, macrolides, metronidazoles, polyketides, quaternary ammonium compounds, streptogramins, sulfonamides, tetracyclines, and trimethoprims as well as resistance transfer genes. The microarray was validated with two fully sequenced control strains of Salmonella enterica: Typhimurium LT2 (sensitive) and Typhi CT18 (multidrug resistance [MDR]). All resistance genes encoded on the MDR plasmid, pHCM1, harbored by CT18 were detected in that strain, whereas no resistance genes were detected in LT2. The microarray was also tested with a variety of bacteria, including MDR Salmonella enterica serovars, Escherichia coli, Campylobacter spp., Enterococcus spp., methicillin-resistant Staphylococcus aureus, Listeria spp., and Clostridium difficile. The results presented here demonstrate that a microarray can be designed to detect virtually all AR genes found in the National Center for Biotechnology Information database, thus reducing the subsequent assays necessary to identify specific resistance gene alleles.

Lindsey, Rebecca L.; Rondeau, Gaelle; Porwollik, Steffen; Long, Fred; McClelland, Michael; Jackson, Charlene R.; Englen, Mark D.; Meinersmann, Richard J.; Berrang, Mark E.; Davis, Johnnie A.; Barrett, John B.; Turpin, Jennifer B.; Thitaram, Sutawee N.; Fedorka-Cray, Paula J.

2010-01-01

129

Identifying contributors of two-person DNA mixtures by familial database search.  

PubMed

The role of familial database search as a crime-solving tool has been increasingly recognized by forensic scientists. As an enhancement to the existing familial search approach on single source cases, this article presents our current progress in exploring the potential use of familial search to mixture cases. A novel method was established to predict the outcome of the search, from which a simple strategy for determining an appropriate scale of investigation by the police force is developed. Illustrated by an example using Swedish data, our approach is shown to have the potential for assisting the police force to decide on the scale of investigation, thereby achieving desirable crime-solving rate with reasonable cost. PMID:22270047

Chung, Yuk-Ka; Fung, Wing K

2012-01-22

130

Does language matter? A case study of epidemiological and public health journals, databases and professional education in French, German and Italian  

PubMed Central

Epidemiology and public health are usually context-specific. Journals published in different languages and countries play a role both as sources of data and as channels through which evidence is incorporated into local public health practice. Databases in these languages facilitate access to relevant journals, and professional education in these languages facilitates the growth of native expertise in epidemiology and public health. However, as English has become the lingua franca of scientific communication in the era of globalisation, many journals published in non-English languages face the difficult dilemma of either switching to English and competing internationally, or sticking to the native tongue and having a restricted circulation among a local readership. This paper discusses the historical development of epidemiology and the current scene of epidemiological and public health journals, databases and professional education in three Western European languages: French, German and Italian, and examines the dynamics and struggles they have today.

Baussano, Iacopo; Brzoska, Patrick; Fedeli, Ugo; Larouche, Claudia; Razum, Oliver; Fung, Isaac C-H

2008-01-01

131

De-identifying a public use microdata file from the Canadian national discharge abstract database  

PubMed Central

Abstract Background The Canadian Institute for Health Information (CIHI) collects hospital discharge abstract data (DAD) from Canadian provinces and territories. There are many demands for the disclosure of this data for research and analysis to inform policy making. To expedite the disclosure of data for some of these purposes, the construction of a DAD public use microdata file (PUMF) was considered. Such purposes include: confirming some published results, providing broader feedback to CIHI to improve data quality, training students and fellows, providing an easily accessible data set for researchers to prepare for analyses on the full DAD data set, and serve as a large health data set for computer scientists and statisticians to evaluate analysis and data mining techniques. The objective of this study was to measure the probability of re-identification for records in a PUMF, and to de-identify a national DAD PUMF consisting of 10% of records. Methods Plausible attacks on a PUMF were evaluated. Based on these attacks, the 2008-2009 national DAD was de-identified. A new algorithm was developed to minimize the amount of suppression while maximizing the precision of the data. The acceptable threshold for the probability of correct re-identification of a record was set at between 0.04 and 0.05. Information loss was measured in terms of the extent of suppression and entropy. Results Two different PUMF files were produced, one with geographic information, and one with no geographic information but more clinical information. At a threshold of 0.05, the maximum proportion of records with the diagnosis code suppressed was 20%, but these suppressions represented only 8-9% of all values in the DAD. Our suppression algorithm has less information loss than a more traditional approach to suppression. Smaller regions, patients with longer stays, and age groups that are infrequently admitted to hospitals tend to be the ones with the highest rates of suppression. Conclusions The strategies we used to maximize data utility and minimize information loss can result in a PUMF that would be useful for the specific purposes noted earlier. However, to create a more detailed file with less information loss suitable for more complex health services research, the risk would need to be mitigated by requiring the data recipient to commit to a data sharing agreement.

2011-01-01

132

GCOD - GeneChip Oncology Database  

Microsoft Academic Search

BACKGROUND: DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has been effectively accessing and using this wealth of data. DESCRIPTION: To address this

Fenglong Liu; Joseph A White; Corina Antonescu; Daniel Gusenleitner; John Quackenbush

2011-01-01

133

Microgravity Database  

NSDL National Science Digital Library

The European Space Agencies (ESA) Microgravity Database "gives scientists access to information regarding all experiments carried out on ESA and NASA missions by European scientists since the 1960s." Users choose from a physical or life sciences query form, then can search by experiment and investigators, mission and facility, publications and source, and more. Results provide the mission name, data, payload, research subject, publication information, an abstract, and any other available facts or related links. A very intuitive and well designed database, visitors should appreciate its unique and extensive content.

2000-01-01

134

ENVIRONMENTAL RESIDUE EFFECTS DATABASE (ERED)  

EPA Science Inventory

US Army Corps of Engineers public web site for the "Environmental Residue Effects Database", a searchable database of adverse biological effects associated with tissue concentrations of various contaminants....

135

Genome databases  

SciTech Connect

Since the Genome Project began several years ago, a plethora of databases have been developed or are in the works. They range from the massive Genome Data Base at Johns Hopkins University, the central repository of all gene mapping information, to small databases focusing on single chromosomes or organisms. Some are publicly available, others are essentially private electronic lab notebooks. Still others limit access to a consortium of researchers working on, say, a single human chromosome. An increasing number incorporate sophisticated search and analytical software, while others operate as little more than data lists. In consultation with numerous experts in the field, a list has been compiled of some key genome-related databases. The list was not limited to map and sequence databases but also included the tools investigators use to interpret and elucidate genetic data, such as protein sequence and protein structure databases. Because a major goal of the Genome Project is to map and sequence the genomes of several experimental animals, including E. coli, yeast, fruit fly, nematode, and mouse, the available databases for those organisms are listed as well. The author also includes several databases that are still under development - including some ambitious efforts that go beyond data compilation to create what are being called electronic research communities, enabling many users, rather than just one or a few curators, to add or edit the data and tag it as raw or confirmed.

Courteau, J.

1991-10-11

136

Drinking Water Treatability Database (Database)  

EPA Science Inventory

The drinking Water Treatability Database (TDB) will provide data taken from the literature on the control of contaminants in drinking water, and will be housed on an interactive, publicly-available USEPA web site. It can be used for identifying effective treatment processes, rec...

137

The co-occurrence of AIDS and homelessness: results from the integration of administrative databases for AIDS surveillance and public shelter utilisation in Philadelphia  

Microsoft Academic Search

STUDY OBJECTIVEAdministrative databases from the City of Philadelphia that track public shelter utilisation (n=44 337) and AIDS case reporting (n=7749) were merged to identify rates and risk factors for co-occurring homelessness and AIDS.DESIGNMultiple decrement life tables analyses were conducted, and logistic regression analyses used to identify risk factors associated with AIDS among the homeless, and homelessness among people with AIDS.SETTINGCity

D P Culhane; E Gollub; R Kuhn; M Shpaner

2001-01-01

138

FULL-malaria: a database for a full-length enriched cDNA library from human malaria parasite, Plasmodium falciparum  

Microsoft Academic Search

FULL-malaria is a database for a full-length-enriched cDNA library from the human malaria parasite Plasmo- dium falciparum (http:\\/\\/133.11.149.55\\/). Because of its medical importance, this organism is the first target for genome sequencing of a eukaryotic pathogen; the sequences of two of its 14 chromosomes have already been determined. However, for the full exploitation of this rapidly accumulating information, correct identification

Junichi Watanabe; Masahide Sasaki; Yutaka Suzuki; Sumio Sugano

2001-01-01

139

Conservation of taxonomic and biological trait diversity of European stream macroinvertebrate communities: a case for a collective public database  

Microsoft Academic Search

The use of databases for the conservation of biodiversity is increasing. During the last decade, such a database has been\\u000a created for European stream macroinvertebrates. Today, it includes 527 sites that are the least human-impacted representatives\\u000a of many stream types across many European regions. It includes data on the abundance of 312 invertebrate genera, several environmental\\u000a site characteristics, collection methods,

Bernhard Statzner; Núria Bonada; Sylvain Dolédec

140

Conservation of taxonomic and biological trait diversity of European stream macroinvertebrate communities: a case for a collective public database  

Microsoft Academic Search

The use of databases for the conservation of biodiversity is increasing. During the last decade, such a database has been\\u000a created for European stream macroinvertebrates. Today, it includes 527 sites that are the least human-impacted representatives\\u000a of many stream types across many European regions. It includes data on the abundance of 312 invertebrate genera, several environmental\\u000a site characteristics, collection methods,

Bernhard Statzner; Núria Bonada; Sylvain Dolédec

2007-01-01

141

Polymorphisms of mtDNA control region in Tunisian and Moroccan populations: an enrichment of forensic mtDNA databases with Northern Africa data.  

PubMed

Current forensic mitochondrial (mt)DNA databases are limited in representative population data of African origin. We investigated HVS-I/HVS-II sequences of 120 Tunisian and Moroccan healthy male donors applying stringent quality criteria to assure high quality of the data and phylogenetic alignment and notation of the sequences. Among 64 Tunisians, 56 different haplotypes were observed and the most common haplotype (16187T 16189C 16223T 16264T 16270T 16278T 16293G 16311C 73G 152C 182T 185T 195C 247A 263G 309.1C 315.1C; haplogroup (hg) L1b) was shared by four individuals. 56 Moroccans could be assigned to 52 different haplotypes where the most common haplotype was of West Eurasian origin with the hg H sequence motif 263G 315.1C and variations in the HVS-II polyC-stretch (309.1C 309.2C) shared by six samples. The majority of the observed haplotypes belong to the west Eurasian phylogeny (50% in Tunisians and 62.5% in Moroccans). Our data are consistent with the current phylogeographic knowledge displaying the occurrence of sub-Saharan haplogroup L sequences, found in 48.4% of Tunisians and 25% of Moroccans as well as the presence of the two re-migrated haplogroups U6 (7.8% and 1.8% in Tunisians and Moroccans, respectively) and M1 (1.6% in Tunisians and 8.9% in Moroccans). PMID:19414164

Turchi, Chiara; Buscemi, Loredana; Giacchino, Erika; Onofri, Valerio; Fendt, Liane; Parson, Walther; Tagliabracci, Adriano

2009-02-25

142

GEOBASE: Israel Regional Database  

NSDL National Science Digital Library

GEOBASE is a searchable database that contains data extracted from Israel's Central Bureau of Statistics, statistical publications, public service records, local databases, and summaries from individual level datasets. GEOBASE provides regularly updated annual and quarterly series on numerous topics, including economic activities, labor and wages, population, transportation, tourism, housing, and education.

1997-01-01

143

The ICRP Database of Dose Coefficients: Workers and Members of the Public, version 1.0 - an extension of ICRP Publications 68 and 72.  

SciTech Connect

A CD-ROM database that gives dose coefficients for inhalation and ingestion of over 800 radionuclides of 91 elements. Inhalation dose coefficients are provided for ten aerosol sizes from 0.001um to 10 um AMAD. Effective dose and equivalent dose coefficients are given for ten integration periods from 1 d to 70y.

Vargo, George J. (BATTELLE (PACIFIC NW LAB))

2000-03-01

144

Global Health Database  

Microsoft Academic Search

The Global Health database is available from Ovid Technologies, Inc., and also from CABI Publishing, EBSCO, and DataStar\\/DIALOG. This database is really the combination of two others—the Public Health and Tropical Medicine database, formerly produced by the Bureau of Hygiene and Tropical Diseases, as well as human health and diseases information that is extracted from the CAB Abstracts database. This

Roberta Bronson Fitzpatrick

2006-01-01

145

q -gram based database searching using a suffix array (QUASAR)  

Microsoft Academic Search

With the increasing amount of DNA sequence informationdeposited in public databases, searching for similarity to aquery sequence has become a basic operation in molecularbiology. But even today's fast algorithms reach theirlimits when applied to all-versus-all comparisons of largedatabases. Here we present a new database searching algorithmcalled QUASAR (Q-gram Alignment based on SuffixARrays) which was designed to quickly detect sequenceswith strong

Stefan Burkhardt; Andreas Crauser; Paolo Ferragina; Hans-Peter Lenhof; Eric Rivals; Martin Vingron

1999-01-01

146

Psychiatric inpatient expenditures and public health insurance programmes: analysis of a national database covering the entire South Korean population  

Microsoft Academic Search

BACKGROUND: Medical spending on psychiatric hospitalization has been reported to impose a tremendous socio-economic burden on many developed countries with public health insurance programmes. However, there has been no in-depth study of the factors affecting psychiatric inpatient medical expenditures and differentiated these factors across different types of public health insurance programmes. In view of this, this study attempted to explore

Woojin Chung

2010-01-01

147

The Institute of Public Administration's Document Center: From Paper to Electronic Records--A Full Image Government Documents Database.  

ERIC Educational Resources Information Center

Since its establishment in 1960, the Institute of Public Administration (IPA) in Riyadh, Saudi Arabia has had responsibility for documenting Saudi administrative literature, the official publications of Saudi Arabia, and the literature of regional and international organizations through establishment of the Document Center in 1961. This paper…

Al-Zahrani, Rashed S.

148

The Institute of Public Administration's Document Center: From Paper to Electronic Records--A Full Image Government Documents Database.  

ERIC Educational Resources Information Center

|Since its establishment in 1960, the Institute of Public Administration (IPA) in Riyadh, Saudi Arabia has had responsibility for documenting Saudi administrative literature, the official publications of Saudi Arabia, and the literature of regional and international organizations through establishment of the Document Center in 1961. This paper…

Al-Zahrani, Rashed S.

149

NATIONAL AND INTERNATIONAL PUBLICATIONS REFLECTED IN BIBLIOMETRIC DATABASES (KRAJOWE I ZGRANICZNE PUBLIKACJE W BIBLIOMETRYCZNYC H BAZACH DANYCH)  

Microsoft Academic Search

Quantifying scientific output is a phenomenon without which science policy and science strategy can no longer be managed. Despite occasional criticism of bibliometric analyses, this tool - when correctly and transpar- ently applied - provides a helpful parameter for science decisions, whereby the publication rate (quantity of publi- cations) and the citation rate (perception of publications) in particular are explored

Rafael Ball; Dirk Tunger

150

The creation of a public database of precision phantoms to facilitate the evaluation and standardization of advanced visualization and quantification software  

NASA Astrophysics Data System (ADS)

In order to validate CT imaging as a biomarker, it is important to ascertain the variability and artifacts associated with various forms of advanced visualization and quantification software. The purpose of the paper is to describe the rationale behind the creation of a free, public resource that contains phantom datasets for CT designed to facilitate testing, development and standardization of advanced visualization and quantification software. For our research, three phantoms were scanned at multiple kVp and mAs settings utilizing a 64-channel MDCT scanner at a collimation of 0.75 mm. Images were reconstructed at a slice thickness of 0.75 mm and archived in DICOM format. The phantoms consisted of precision spheres, balls of different materials and sizes, and slabs of Last-A-Foam(R) at varying densities. The database of scans is stored in an archive utilizing software developed for the National Cancer Imaging Archive and is publically available. The scans were completed successfully and the datasets are available for free and unrestricted download. The CT images can be accessed in DICOM format via http or FTP or utilizing caGRID. A DICOM database of phantom data was successfully created and made available to the public. We anticipate that this database will be useful as a reference for physicists for quality control purposes, for developers of advanced visualization and quantification software, and for others who need to test the performance of their systems against a known "gold" standard. We plan to add more phantom images in the future and expand to other imaging modalities.

Chen, Joseph J.; Saenz, Naomi J.; Siegel, Eliot L.

2009-02-01

151

The ICRP database of dose coefficients: Workers and members of the public, version 1.0, an extension of ICRP publications 68 and 72  

Microsoft Academic Search

A CDROM database that gives dose coefficients for inhalation and ingestion of over 800 radionuclides of 91 elements. Inhalation dose coefficients are provided for ten aerosol sizes from 0.001 μm to 10 μm AMAD. Effective dose and equivalent dose coefficients are given for ten integration periods form 1 d to 70 y. Extensive help files summarizing the biokinetic models in

George J. Vargo; George J

2000-01-01

152

DATARIs: Database on Research Institutes  

NSDL National Science Digital Library

The United Nations Institute for Disarmament Research (UNIDIR), in cooperation with the Stockholm International Peace Research Institute (SIPRI), maintain DATARIs, a collection of databases providing information from and about research institutes specializing in international relations and security. DATARIs includes directory databases on research institutes and documentation centers, bibliographic databases on research institute projects and publications, and a database providing information about databases maintained by associated research institutes. Each searchable database offers an easy-to-use search form interface, facilitating queries for users.

1998-01-01

153

The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data  

Microsoft Academic Search

Substantial new features have been implemented at the Ribosomal Database Project in response to the increased importance of high-throughput rRNA sequence analysis in microbial ecology and related disciplines. The most important changes include quality analysis, including chimera detection, for all available rRNA sequences and the introduction of myRDP Space, a new web component designed to help researchers place their own

James R. Cole; B. Chai; Ryan J. Farris; Q. Wang; A. S. Kulam-syed-mohideen; D. M. Mcgarrell; A. M. Bandela; E. Cardenas; George M. Garrity; James M. Tiedje

2007-01-01

154

MetIDB: A Publicly Accessible Database of Predicted and Experimental (1)H NMR Spectra of Flavonoids.  

PubMed

Identification of natural compounds, especially secondary metabolites, has been hampered by the lack of easy to use and accessible reference databases. Nuclear magnetic resonance (NMR) spectroscopy is the most selective technique for identification of unknown metabolites. High quality (1)H NMR (proton nuclear magnetic resonance) spectra combined with elemental composition obtained from mass spectrometry (MS) are essential for the identification process. Here, we present MetIDB, a reference database of experimental and predicted (1)H NMR spectra of 6000 flavonoids. By incorporating the stereochemistry, intramolecular interactions, and solvent effects into the prediction model, chemical shifts and couplings were predicted with great accuracy. A user-friendly web-based interface for MetIDB has been established providing various interfaces to the data and data-mining possibilities. For each compound, additional information is available comprising compound annotation, a (1)H NMR spectrum, 2D and 3D structure with correct stereochemistry, and monoisotopic mass as well as links to other web resources. The combination of chemical formula and (1)H NMR chemical shifts proved to be very efficient in metabolite identification, especially for isobaric compounds. Using this database, the process of flavonoid identification can then be significantly shortened by avoiding repetitive elucidation of already described compounds. PMID:23930710

Mihaleva, Velitchka V; Te Beek, Tim A H; van Zimmeren, Frank; Moco, Sofia; Laatikainen, Reino; Niemitz, Matthias; Korhonen, S-P; van Driel, Marc A; Vervoort, Jacques

2013-08-26

155

Human Mitochondrial Protein Database  

NSDL National Science Digital Library

The Human Mitochondrial Protein Database (HMPDb) conveniently consolidates information from a number of other databases, including GenBank, Online Mendelian Inheritance in Man, and the Human Mitochondrial Genome Database. HMPDb "is intended as a tool not only to aid in studying the mitochondrion but in studying the associated diseases" as well. Features include a general database search, a graphical tool for visualizing the mitochondrial DNA sequences, and 3D structures for mitochondrial proteins. Users are welcome to contact the National Institute of Standards and Technology with corrections or other information relating to the database.

156

Biological Biochemical Image Database  

NSDL National Science Digital Library

The National Institute on Aging -- one of the National Institutes of Health -- provides the Biological Biochemical Image Database, "a searchable database of images of putative biological pathways, macromolecular structures, gene families, and cellular relationships." The database is intended for researchers "working with large sets of genes or proteins using cDNA arrays, functional genomics, or proteomics." The database may be searched by gene name, pathway, cell or tissue type, disease name, biological level, etc. Database users are invited to submit additional diagrams, suggestions, and comments The Web site also includes convenient lists of gene names and keywords, as well as links to biological/ biochemical pathway Web resources.

157

Global health database.  

PubMed

The Global Health database is available from Ovid Technologies, Inc., and also from CABI Publishing, EBSCO, and DataStar/ DIALOG. This database is really the combination of two others--the Public Health and Tropical Medicine database, formerly produced by the Bureau of Hygiene and Tropical Diseases, as well as human health and diseases information that is extracted from the CAB Abstracts database. This column will provide readers with an overview of the Global Health database, as well as present some searching hints. The Ovid interface will be used. PMID:16782667

Fitzpatrick, Roberta Bronson

2006-01-01

158

Evaluating Statistical Methods Using Plasmode Data Sets in the Age of Massive Public Databases: An Illustration Using False Discovery Rates  

Microsoft Academic Search

Plasmode is a term coined several years ago to describe data sets that are derived from real data but for which some truth is known. Omic techniques, most especially microarray and genomewide association studies, have catalyzed a new zeitgeist of data sharing that is making data and data sets publicly available on an unprecedented scale. Coupling such data resources with

Gary L. Gadbury; Qinfang Xiang; Lin Yang; Stephen Barnes; Grier P. Page; David B. Allison

2008-01-01

159

FLAGdb\\/FST: a database of mapped flanking insertion sites (FSTs) of Arabidopsis thaliana T-DNA transformants  

Microsoft Academic Search

A large collection of T-DNA insertion transformants of Arabidopsis thaliana has been generated at the Institute of Agronomic Research, Versailles, France. The molecular characterisation of the insertion sites is currently performed by sequencing genomic regions flanking the inserted T-DNA (FST). The almost complete sequence of the nuclear genome of A.thaliana provides the framework for organising FSTs in a genome oriented

Franck Samson; Véronique Brunaud; Sandrine Balzergue; B. Dubreucq; L. Lepiniec; G. Pelletier; Michel Caboche; Alain Lecharny

2002-01-01

160

EDGEdb: a transcription factor-DNA Interaction database for the analysis of C. elegans differential gene expression  

Microsoft Academic Search

BACKGROUND: Transcription regulatory networks are composed of protein-DNA interactions between transcription factors and their target genes. A long-term goal in genome biology is to map protein-DNA interaction networks of all regulatory regions in a genome of interest. Both transcription factor -and gene-centered methods can be used to systematically identify such interactions. We use high-throughput yeast one-hybrid assays as a gene-centered

M Inmaculada Barrasa; Philippe Vaglio; Fabien Cavasino; Laurent Jacotot; Albertha JM Walhout

2007-01-01

161

Identification of new eukaryotic tRNA genes in genomic DNA databases by a multistep weight matrix analysis of transcriptional control regions.  

PubMed Central

A linear method for the search of eukaryotic nuclear tRNA genes in DNA databases is described. Based on a modified version of the general weight matrix procedure, our algorithm relies on the recognition of two intragenic control regions known as A and B boxes, a transcription termination signal, and on the evaluation of the spacing between these elements. The scanning of the eukaryotic nuclear DNA database using this search algorithm correctly identified 933 of the 940 known tRNA genes (0.74% of false negatives). Thirty new potential tRNA genes were identified, and the transcriptional activity of two of them was directly verified by in vitro transcription. The total false positive rate of the algorithm was 0.014%. Structurally unusual tRNA genes, like those coding for selenocysteine tRNAs, could also be recognized using a set of rules concerning their specific properties, and one human gene coding for such tRNA was identified. Some of the newly identified tRNA genes were found in rather uncommon genomic positions: 2 in centromeric regions and 3 within introns. Furthermore, the presence of extragenically located B boxes in tRNA genes from various organisms could be detected through a specific subroutine of the standard search program. Images

Pavesi, A; Conterio, F; Bolchi, A; Dieci, G; Ottonello, S

1994-01-01

162

Citation analysis of publications of NASU mechanicians in the database of the Thomson Reuters Institute for Scientific Information  

Microsoft Academic Search

The paper performs a citation analysis of publications of mechanicians of the National Academy of Sciences of Ukraine (NASU)\\u000a based on information tools developed by the Thomson Reuters Institute for Scientific Information. Two groups of mechanicians\\u000a are considered: representatives of the S. P. Timoshenko Institute of Mechanics of the NASU (NASU members, heads of departments)\\u000a and members (academicians) of the

A. N. Guz; J. J. Rushchitsky

2009-01-01

163

Selected Publications & Presentations  

Center for Food Safety and Applied Nutrition (CFSAN)

... Selected Publications & Presentations. Recent Food Research Publications and FDA Publications Database. 2008 Intramural Research Portfolio. ... More results from www.fda.gov/food/foodscienceresearch/toolsmaterials

164

Psychiatric inpatient expenditures and public health insurance programmes: analysis of a national database covering the entire South Korean population  

PubMed Central

Background Medical spending on psychiatric hospitalization has been reported to impose a tremendous socio-economic burden on many developed countries with public health insurance programmes. However, there has been no in-depth study of the factors affecting psychiatric inpatient medical expenditures and differentiated these factors across different types of public health insurance programmes. In view of this, this study attempted to explore factors affecting medical expenditures for psychiatric inpatients between two public health insurance programmes covering the entire South Korean population: National Health Insurance (NHI) and National Medical Care Aid (AID). Methods This retrospective, cross-sectional study used a nationwide, population-based reimbursement claims dataset consisting of 1,131,346 claims of all 160,465 citizens institutionalized due to psychiatric diagnosis between January 2005 and June 2006 in South Korea. To adjust for possible correlation of patients characteristics within the same medical institution and a non-linearity structure, a Box-Cox transformed, multilevel regression analysis was performed. Results Compared with inpatients 19 years old or younger, the medical expenditures of inpatients between 50 and 64 years old were 10% higher among NHI beneficiaries but 40% higher among AID beneficiaries. Males showed higher medical expenditures than did females. Expenditures on inpatients with schizophrenia as compared to expenditures on those with neurotic disorders were 120% higher among NHI beneficiaries but 83% higher among AID beneficiaries. Expenditures on inpatients of psychiatric hospitals were greater on average than expenditures on inpatients of general hospitals. Among AID beneficiaries, institutions owned by private groups treated inpatients with 32% higher costs than did government institutions. Among NHI beneficiaries, inpatients medical expenditures were positively associated with the proportion of patients diagnosed into dementia or schizophrenia categories. However, for AID beneficiaries, inpatient medical expenditures were positively associated with the proportion of all patients with a psychiatric diagnosis that were AID beneficiaries in a medical institution. Conclusions This study provides evidence that patient and institutional factors are associated with psychiatric inpatient medical expenditures, and that they may have different effects for beneficiaries of different public health insurance programmes. Policy efforts to reduce psychiatric inpatient medical expenditures should be made differently across the different types of public health insurance programmes.

2010-01-01

165

Who owns what? Private ownership and the public interest in recombinant DNA technology in the 1970s.  

PubMed

This essay analyzes how academic institutions, government agencies, and the nascent biotech industry contested the legal ownership of recombinant DNA technology in the name of the public interest. It reconstructs the way a small but influential group of government officials and university research administrators introduced a new framework for the commercialization of academic research in the context of a national debate over scientific research's contributions to American economic prosperity and public health. They claimed that private ownership of inventions arising from public support would provide a powerful means to liberate biomedical discoveries for public benefit. This articulation of the causal link between private ownership and the public interest, it is argued, justified a new set of expectations about the use of research results arising from government or public support, in which commercialization became a new public obligation for academic researchers. By highlighting the broader economic and legal shifts that prompted the reconfiguration of the ownership of public knowledge in late twentieth-century American capitalism, the essay examines the threads of policy-informed legal ideas that came together to affirm private ownership of biomedical knowledge as germane to the public interest in the coming of age of biotechnology and genetic medicine. PMID:22073770

Yi, Doogab

2011-09-01

166

The PNNL quantitative infrared database for gas-phase sensing: a spectral library for environmental, hazmat, and public safety standoff detection  

NASA Astrophysics Data System (ADS)

Pacific Northwest National Laboratory (PNNL) continues to expand its library of quantitative infrared reference spectra for remote sensing. The gas-phase data are recorded at 0.1 cm-1 resolution, with nitrogen pressure broadening to one atmosphere to emulate spectra recorded in the field. It is planned that the PNNL library will consist of approximately 500 vapor-phase spectra associated with the U.S. Department of Energy"s environmental, energy, and public safety missions. At present, the database is comprised of approximately 300 infrared spectra, many of which represent highly reactive or toxic species. For the 298 K data, each reported spectrum is in fact a composite spectrum generated by a Beer"s law plot (at each wavelength) to typically 12 measured spectra. Recent additions to the database include the vapors of several semi-volatile and non-volatile liquids using an improved dissemination technique for vaporizing the liquid into the nitrogen carrier gas. Experimental and analytical methods are used to remove several known and new artifacts associated with FTIR gas-phase spectroscopy. Details concerning sample preparation and composite spectrum generation are discussed.

Johnson, Timothy J.; Sams, Robert L.; Sharpe, Steven W.

167

The PNNL Quantitative Infrared Database for Gas-Phase Sensing: A spectral Library for Environmental, Hazmat, and Public Safety Standoff Detection  

SciTech Connect

Pacific Northwest National Laboratory (PNNL) continues to expand its library of quantitative infrared reference spectra for remote sensing. The gas-phase data are recorded at 0.1 cm-1 resolution, with nitrogen pressure broadening to one atmosphere to emulate spectra recorded in the field. It is planned that the PNNL library will consist of approximately 500 vapor-phase spectra associated with the U.S. Department of Energy's environmental, energy, and public safety missions. At present, the database is comprised of approximately 300 infrared spectra, many of which represent highly reactive or toxic species. For the 298 K data, each reported spectrum is in fact a composite spectrum generated by a Beer's law plot (at each wavelength) to typically 12 measured spectra. Recent additions to the database include the vapors of several semi-volatile and non-volatile liquids using an improved dissemination technique for vaporizing the liquid into the nitrogen carrier gas. Experimental and analytical methods are used to remove several known and new artifacts associated with FTIR gas-phase spectroscopy. Details concerning sample preparation and composite spectrum generation are discussed.

Johnson, Timothy J.; Sams, Robert L.; Sharpe, Steven W.; Arthur J. Sedlacek III, Richard Colton, Tuan Vo-Dinh

2004-03-25

168

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools.  

PubMed

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance. PMID:23125372

Cer, Regina Z; Donohue, Duncan E; Mudunuri, Uma S; Temiz, Nuri A; Loss, Michael A; Starner, Nathan J; Halusa, Goran N; Volfovsky, Natalia; Yi, Ming; Luke, Brian T; Bacolla, Albino; Collins, Jack R; Stephens, Robert M

2012-11-03

169

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools  

PubMed Central

The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted non-B DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted repeats, mirror repeats, direct repeats and their corresponding subsets: cruciforms, triplexes and slipped structures, in several genomes. Version 2.0 of the database revises and re-implements the motif discovery algorithms to better align with accepted definitions and thresholds for motifs, expands the non-B DNA-forming motifs coverage by including short tandem repeats and adds key visualization tools to compare motif locations relative to other genomic annotations. Non-B DB v2.0 extends the ability for comparative genomics by including re-annotation of the five organisms reported in non-B DB v1.0, human, chimpanzee, dog, macaque and mouse, and adds seven additional organisms: orangutan, rat, cow, pig, horse, platypus and Arabidopsis thaliana. Additionally, the non-B DB v2.0 provides an overall improved graphical user interface and faster query performance.

Cer, Regina Z.; Donohue, Duncan E.; Mudunuri, Uma S.; Temiz, Nuri A.; Loss, Michael A.; Starner, Nathan J.; Halusa, Goran N.; Volfovsky, Natalia; Yi, Ming; Luke, Brian T.; Bacolla, Albino; Collins, Jack R.; Stephens, Robert M.

2013-01-01

170

The feasibility of storing ovarian tumor cells on databasing paper: establishing a library of ovarian cancer DNA.  

PubMed

The purpose of this study was to assess the feasibility of establishing a library of ovarian cancer nucleic acids using paper matrix by: 1) confirming the stability of DNA stored on paper matrix over a prolonged period of time, 2) determining the amount of genetic material required for storage, and 3) establishing the stability of RNA. Tumor tissue from 66 patients with ovarian cancer was collected intraoperatively, frozen, and dissociated with collagenase and trypsin. A cell suspension was then prepared and spotted onto the paper. The numbers of cells that were stored on the paper were counted using a hemocytometer. The cell suspension was serially diluted and spotted on the paper matrix until the minimum cell number that can be stored and produce a PCR product was determined. PCR, STR genotyping and direct sequencing were performed on tissue stored on the paper matrix. FTA paper was used as RNA template, and RT PCR converted the RNA to cDNA. Ten to 50 mg of ovarian cancer tissue was stored on FTA paper. We stored 7 x 10(4) cells on ISOcode paper and 18 x 10(4) cells on FTA and obtained extractable DNA. PCR analysis on cards with DNA stored 18 months ago enabled us to establish the stability of DNA after storage. RNA was stable for 6 months when stored on FTA cards. Since genetic material is extractable from the paper matrices after passage of time, it could be a suitable medium for the storage of genetic material in cancer tissue banks. PMID:17291238

Galaal, K; Meirovitz, M; Hussain, R; Allcroft, L; Sullivan, N; Lopes, A; Edmondson, R J

171

HS3D, A Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database  

NASA Astrophysics Data System (ADS)

The aim of this work is to describe a cleaning procedure of GenBank data, producing material to train and to assess the prediction accuracy of computational approaches for gene characterization. A procedure (GenBank2HS3D) has been defined, producing a dataset (HS3D - Homo Sapiens Splice Sites Dataset) of Homo Sapiens Splice regions extracted from GenBank (Rel.123 at this time). It selects, from the complete GenBank Primate Division, entries of Human Nuclear DNA according with several assessed criteria; then it extracts exons and introns from these entries (actually 4523 + 3802). Donor and acceptor sites are then extracted as windows of 140 nucleotides around each splice site (3799 + 3799). After discarding windows not including canonical GT-AG junctions (65 + 74), including insufficient data (not enough material for a 140 nucleotide window) (686 + 589), including not AGCT bases (29 + 30), and redundant (218 + 226), the remaining windows (2796 + 2880) are reported in the dataset. Finally, windows of false splice sites are selected by searching canonical GT-AG pairs in not splicing positions (271 937 + 332 296). The false sites in a range +/- 60 from a true splice site are marked as proximal. HS3D, release 1.2 at this time, is available at the Web server of the University of Sannio: http://www.sci.unisannio.it/docenti/rampone/.

Pollastro, Pasquale; Rampone, Salvatore

172

GCOD - GeneChip Oncology Database  

PubMed Central

Background DNA microarrays have become a nearly ubiquitous tool for the study of human disease, and nowhere is this more true than in cancer. With hundreds of studies and thousands of expression profiles representing the majority of human cancers completed and in public databases, the challenge has been effectively accessing and using this wealth of data. Description To address this issue we have collected published human cancer gene expression datasets generated on the Affymetrix GeneChip platform, and carefully annotated those studies with a focus on providing accurate sample annotation. To facilitate comparison between datasets, we implemented a consistent data normalization and transformation protocol and then applied stringent quality control procedures to flag low-quality assays. Conclusion The resulting resource, the GeneChip Oncology Database, is available through a publicly accessible website that provides several query options and analytical tools through an intuitive interface.

2011-01-01

173

Nanotechnology Database  

NSDL National Science Digital Library

Sponsored by the National Science Foundation and housed at the Loyola College in Maryland's International Technology Research Institute the Nanotechnology Database is a source of online information on major research centers, funding agencies, major reports, and books dealing with nanotechnology. The resources listed here are carefully selected and reviewed. The site is expected to grow with the continued support and updates from organizations and individuals in the field of nanotechnology. The list of resources is divided into the following categories: Academic, Industry, Government Laboratories, Government Agencies, Professional Societies, Non-Profit Organizations, Books, Periodicals, Reports, and Conferences. Each listing provides a brief summary (taken from that Website) and hyperlink to the resource (note: the book list links mostly take users to online booksellers). A submission form allows users to add a relevant organization or publication.

2001-01-01

174

Bibliometric assessment of publication output of child and adolescent psychiatric/psychological affiliations between 2005 and 2010 based on the databases PubMed and Scopus.  

PubMed

We aimed to determine the quantitative scientific publication output of child and adolescent psychiatric/psychological affiliations during 2005-2010 by country based on both, "PubMed" and "Scopus" and performed a bibliometric qualitative evaluation for 2009 using "PubMed". We performed our search by affiliation related to child and adolescent psychiatric/psychological institutions using "PubMed". For the quantitative analysis for 2005-2010, we counted the number of abstracts. For the qualitative analysis for 2009 we derived the impact factor of each abstract's journal from "Journal Citation Reports". We related total impact factor scores to the gross domestic product (GDP) and population size of each country. Additionally, we used "Scopus" to determine the number of abstracts for each country that was identified via "PubMed" for 2009 and compared the ranking of countries between the two databases. 61 % of the publications between 2005 and 2010 originated from European countries and 26 % from the USA. After adjustment for GDP and population size, the ranking positions changed in favor of smaller European countries with a population size of less than 20 million inhabitants. The ranking of countries for the count of articles in 2009 as derived from "Scopus" was similar to that identified via the "PubMed" search. The performed search revealed only minor differences between "Scopus" and "PubMed" related to the ranking of countries. Our data indicate a sharp difference between countries with a high versus low GDP with regard to scientific publication output in child and adolescent psychiatry/psychology. PMID:22434265

Albayrak, Ozgür; Föcker, Manuel; Wibker, Katrin; Hebebrand, Johannes

2012-03-21

175

Rainfall Simulation Database  

NSDL National Science Digital Library

The British Geomorphological Research Group maintains this rainfall simulation database site. The database includes information about rainfall simulators, as well as their set-up and use. Currently, the database is divided into laboratory, field, and dual-purpose (lab and field) rainfall simulators. For each simulator in the database, users will find information on: "Simulator identification; Contact information; Specification of simulator; performance of simulator; Table of intensities and rainfall characteristics; Costs; Summary of research conducted using the simulator; Publications; and Additional comments." A section on simulation calibration is planned, and a form is provided for those wishing to contribute simulators to the database. A lengthy selection of related references adds to the utility of the database.

176

Contamination of sequence databases with adaptor sequences  

SciTech Connect

Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)

1997-02-01

177

Curated databases  

Microsoft Academic Search

Curated databases are databases that are populated and updated with a great deal of human effort. Most reference works that one traditionally found on the reference shelves of libraries -- dictionaries, encyclopedias, gazetteers etc. -- are now curated databases. Since it is now easy to publish databases on the web, there has been an explosion in the number of new

Peter Buneman; James Cheney; Wang-Chiew Tan; Stijn Vansummeren

2008-01-01

178

Buffmap Database  

NSDL National Science Digital Library

The Institut National de Recherche Agronomique (France) provides online databases of genomes for several organisms, including Buffalo. The database is updated as more data become available, and provide records on loci, genes, microsatellites, polymorphisms, probes, enzymes, homologue loci, alleles, primers, references, and links to external databases. Instructions for submitting data to the databases are provided on-site.

179

Method and system for normalizing biometric variations to authenticate users from a public database and that ensures individual biometric data privacy  

DOEpatents

A password system comprises a set of codewords spaced apart from one another by a Hamming distance (HD) that exceeds twice the variability that can be projected for a series of biometric measurements for a particular individual and that is less than the HD that can be encountered between two individuals. To enroll an individual, a biometric measurement is taken and exclusive-ORed with a random codeword to produce a "reference value." To verify the individual later, a biometric measurement is taken and exclusive-ORed with the reference value to reproduce the original random codeword or its approximation. If the reproduced value is not a codeword, the nearest codeword to it is found, and the bits that were corrected to produce the codeword to it is found, and the bits that were corrected to produce the codeword are also toggled in the biometric measurement taken and the codeword generated during enrollment. The correction scheme can be implemented by any conventional error correction code such as Reed-Muller code R(m,n). In the implementation using a hand geometry device an R(2,5) code has been used in this invention. Such codeword and biometric measurement can then be used to see if the individual is an authorized user. Conventional Diffie-Hellman public key encryption schemes and hashing procedures can then be used to secure the communications lines carrying the biometric information and to secure the database of authorized users.

Strait, Robert S. (Oakland, CA); Pearson, Peter K. (Livermore, CA); Sengupta, Sailes K. (Livermore, CA)

2000-01-01

180

Publications  

Cancer.gov

Publications News Updates PLCO Update Suggests Positive Predictive Value of Prostate Screening Drops over Time (Posted 01/13/2009) Report from Large NCI Study Suggests PSA Testing Could Be Done at Longer Intervals for Men Who Choose to Test(Posted

181

Publications  

Cancer.gov

Publications View All  |  2013-2010  |  2009-2000  |  1999-1990  |  1989-1980  |  1979-1970 2013 2012 2011 2010 Baker SG, Kramer BS. Surrogate endpoint analysis: an exercise in extrapolation. J Natl Cancer Inst 2013;105(5):316-320.[ PubMed

182

Database Administrator  

ERIC Educational Resources Information Center

|The Internet and electronic commerce (e-commerce) generate lots of data. Data must be stored, organized, and managed. Database administrators, or DBAs, work with database software to find ways to do this. They identify user needs, set up computer databases, and test systems. They ensure that systems perform as they should and add people to the…

Moore, Pam

2010-01-01

183

Hydrocarbon Impacts Database  

NSDL National Science Digital Library

The Hydrocarbon Impacts (HI) database is a subset of the University of Calgary's Arctic Institute of North America's Arctic Science and Technology Information System database. More than 5,100 records describe "publications and research projects about the environmental impacts, socio-economic effects and regulation of hydrocarbon exploration, development and transportation in northern Canada." Users can search by record type, keyword, subject code, geographic code, author, and year, as well as an advanced search feature to locate the information. Well designed and easy to use, the database provides those interested in this narrow subject field a helpful resource.

184

ESTuber db: an online database for Tuber borchii EST sequences  

Microsoft Academic Search

BACKGROUND: The ESTuber database (http:\\/\\/www.itb.cnr.it\\/estuber) includes 3,271 Tuber borchii expressed sequence tags (EST). The dataset consists of 2,389 sequences from an in-house prepared cDNA library from truffle vegetative hyphae, and 882 sequences downloaded from GenBank and representing four libraries from white truffle mycelia and ascocarps at different developmental stages. An automated pipeline was prepared to process EST sequences using public

Barbara Lazzari; Andrea Caprera; Cristian Cosentino; Alessandra Stella; Luciano Milanesi; Angelo Viotti

2007-01-01

185

Russian Regional Database  

NSDL National Science Digital Library

The Centre for the Study of Public Policy (CSPP) at the University of Strathclyde, Glasgow has created a new online database that presents a comparative overview of eleven Russian regions: Central, Central Black Earth, East Siberia, Far East, North Caucasus, Northern, North-west, Urals, Volga, Volgo-Vyatka, and West Siberia. The database provides data garnered from official government statistics and public opinion surveys to compare indicators that measure economic competitiveness; labor market change; and social cohesion, exclusion, and stability. The data are accompanied by analysis written by Professor Richard Rose.

1998-01-01

186

The Diatom EST Database.  

PubMed

The Diatom EST database provides integrated access to expressed sequence tag (EST) data from two eukaryotic microalgae of the class Bacillariophyceae, Phaeodactylum tricornutum and Thalassiosira pseudonana. The database currently contains sequences of close to 30,000 ESTs organized into PtDB, the P.tricornutum EST database, and TpDB, the T.pseudonana EST database. The EST sequences were clustered and assembled into a non-redundant set for each organism, and these non-redundant sequences were then subjected to automated annotation using similarity searches against protein and domain databases. EST sequences, clusters of contiguous sequences, their annotation and analysis with reference to the publicly available databases, and a codon usage table derived from a subset of sequences from PtDB and TpDB can all be accessed in the Diatom EST Database. The underlying RDBMS enables queries over the raw and annotated EST data and retrieval of information through a user-friendly web interface, with options to perform keyword and BLAST searches. The EST data can also be retrieved based on Pfam domains, Cluster of Orthologous Groups (COG) and Gene Ontologies (GO) assigned to them by similarity searches. The Database is available at http://avesthagen.sznbowler.com. PMID:15608213

Maheswari, Uma; Montsant, Anton; Goll, Johannes; Krishnasamy, S; Rajyashri, K R; Patell, Villoo Morawala; Bowler, Chris

2005-01-01

187

Public concern over genetic manipulation, Alexander CapronSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

Alexander Capron DNAi Location:Manipulation>Revolution>players>The controversy The Frankenstein factor Alexander Capron, a lawyer and specialist in bioethics, talks about how fear of Frankenstein captured the public fancy.

2008-10-06

188

IOPI Database of Plant Databases  

NSDL National Science Digital Library

The International Organization for Plant Information (IOPI), a Commission of the International Union of Biological Sciences (IUBS), manages the Database of Plant Databases (DPD). The DPD is a global list of plant databases including Taxonomic databases ("with systematic information on families or genera, or for Flora projects"); Collection catalogs (usually of herbaria); and DELTA datasets (DELTA is "the Description Language for Taxonomy, a data format for character data, used for identification, key construction and the generation of descriptions."). The DPD may be searched using numerous specified fields, or it may be viewed in its entirety -- by Database Name, Host Name, or Host Country. Though bare bones in appearance, this extensive database contains a gold mine of information, with hundreds of hyperlinks to valuable plant databases.

189

The EMBL Nucleotide Sequence Database  

Microsoft Academic Search

The European Molecular Biology Laboratory (EMBL) Nucleotide Sequence Database (http:\\/\\/www.ebi.ac. uk\\/embl\\/index.html ) is maintained at the European Bioinformatics Institute (EBI) in an international collaboration with the DNA Data Bank of Japan (DDBJ) and GenBank (USA). Data is exchanged amongst the collaborative databases on a daily basis. The major contributors to the EMBL database are individual authors and genome project groups.

Wendy Baker; Alexandra Van Den Broek; Evelyn Camon; Pascal Hingamp; Peter Sterk; Guenter Stoesser; Mary Ann Tuli

2000-01-01

190

READ: RIKEN Expression Array Database  

Microsoft Academic Search

READ, the RIKEN Expression Array Database, is a database of expression profile data from the RIKEN mouse cDNA microarray. It stores the microarray experimental data and information, and provides Web interfaces for researchers to use to retrieve, analyze and display their data. The goals for READ are to serve as a storage site for microarray data from ongoing research in

Hidemasa Bono; Takeya Kasukawa; Yoshihide Hayashizaki; Yasushi Okazaki

2002-01-01

191

National Ambient Radiation Database  

SciTech Connect

The U.S. Environmental Protection Agency (EPA) recently developed a searchable database and website for the Environmental Radiation Ambient Monitoring System (ERAMS) data. This site contains nationwide radiation monitoring data for air particulates, precipitation, drinking water, surface water and pasteurized milk. This site provides location-specific as well as national information on environmental radioactivity across several media. It provides high quality data for assessing public exposure and environmental impacts resulting from nuclear emergencies and provides baseline data during routine conditions. The database and website are accessible at www.epa.gov/enviro/. This site contains (1) a query for the general public which is easy to use--limits the amount of information provided, but includes the ability to graph the data with risk benchmarks and (2) a query for a more technical user which allows access to all of the data in the database, (3) background information on ER AMS.

Dziuban, J.; Sears, R.

2003-02-25

192

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA  

PubMed Central

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in their nucleotide composition and consist of a complex mosaic of sequence patterns. These patterns include so-called Mid-Range Inhomogeneity (MRI) regions -- sequences 30-10000 nucleotides in length that are enriched by a particular base or combination of bases (e.g. (G+T)-rich, purine-rich, etc.). MRI regions are associated with unusual (non-B-form) DNA structures that are often involved in regulation of gene expression, recombination, and other genetic processes (Fedorova & Fedorov 2010). The existence of a strong fixation bias within MRI regions against mutations that tend to reduce their sequence inhomogeneity additionally supports the functionality and importance of these genomic sequences (Prakash et al. 2009). Here we demonstrate a freely available Internet resource -- the Genomic MRI program package -- designed for computational analysis of genomic sequences in order to find and characterize various MRI patterns within them (Bechtel et al. 2008). This package also allows generation of randomized sequences with various properties and level of correspondence to the natural input DNA sequences. The main goal of this resource is to facilitate examination of vast regions of non-coding DNA that are still scarcely investigated and await thorough exploration and recognition.

Prakash, Ashwin; Bechtel, Jason; Fedorov, Alexei

2011-01-01

193

Database Language SQL. Category: Software Standard. Subcategory: Database, June 1993.  

National Technical Information Service (NTIS)

The publication announces adoption of American National Standard Database Language SQL, ANSI X3.135-1992, as the Federal Information Processing Standard for Database Language SQL (FIPS SQL). It is a revision of FIPS PUB 127-1 that adds extensive new funct...

1993-01-01

194

Database replication  

US Patent & Trademark Office Database

A new database design is implemented in which everything in the database is modeled with primitives, including the links and nodes for a graph tuple store. A query syntax provides a nested tree of constraints with a single global schema. Various optimization techniques for queries and replication techniques are also described.

2012-06-19

195

Image Databases.  

ERIC Educational Resources Information Center

Different kinds of pictorial databases are described with respect to aims, user groups, search possibilities, storage, and distribution. Some specific examples are given for databases used for the following purposes: (1) labor markets for artists; (2) document management; (3) telling a story; (4) preservation (archives and museums); (5) research;…

Pettersson, Rune

196

NSFC Databases  

NSDL National Science Digital Library

The National Environmental Services Center (NESC) is based at West Virginia University and "serves as a clearinghouse for information about drinking water, wastewater, environmental training, and solid waste management in communities serving fewer than 10,000 individuals." As part of the NSFC larger Web site, the Databases page offers three online databases that can be accessed free after an initial registration. The Regulations Database contains copies of regulations for onsite wastewater treatment systems in 48 states, the Bibliographic Database stores thousands of articles dealing with onsite and small community wastewater issues, and the Manufacturers and Consultants Database houses a list of industry contacts for wastewater products and consulting services. Much more is available within the larger NSFC site and readers are encouraged to take a look through its contents.

2001-01-01

197

JICST Factual Database(1)  

NASA Astrophysics Data System (ADS)

The outline of JICST factual database (JOIS-F), which JICST has started from January, 1988, and its online service are described in this paper. First, the author mentions the circumstances from 1973, when its planning was started, to the present, and its relation to "Project by Special Coordination Founds for Promoting Science and Technology". Secondly, databases, which are now under development aiming to start its services from fiscal 1988 or fiscal 1989, of DNA, metallic material intensity, crystal structure, chemical substance regulations, and so forth, are described. Lastly, its online service is briefly explained.

Kurosawa, Shinji

198

BIOMARKERS DATABASE  

EPA Science Inventory

This database was developed by assembling and evaluating the literature relevant to human biomarkers. It catalogues and evaluates the usefulness of biomarkers of exposure, susceptibility and effect which may be relevant for a longitudinal cohort study. In addition to describing ...

199

Ant Database  

NSDL National Science Digital Library

Research entomologist Ted Schultz from the Smithsonian Institution maintains this impressive work in progress. This online database represents the Smithsonian's identified ant collection, including 4,580 valid named species or subspecies. The taxonomy is current with Bolton's 1995 catalog and includes reported holdings through June 1998. The database may be queried by Subfamily, Tribe, Genus, Subgenus, Species, Subspecies, Author, or Types, and typical returns give concise taxonomic information, total specimens (workers, females, and males), author, and year.

Schultz, Ted.

2000-01-01

200

DNA  

ERIC Educational Resources Information Center

|This history for molecular genetics and its explanation of DNA begins with an analysis of the Golden Jubilee essay papers, 1955. The paper ends stating that the higher nervous system is the one major frontier of biological inquiry which still offers some romance of research. (Author/VW)|

Stent, Gunther S.

1970-01-01

201

NUCLEAR DATABASES FOR REACTOR APPLICATIONS.  

SciTech Connect

The National Nuclear Data Center (NNDC): An overview of nuclear databases, related products, nuclear data Web services and publications. The NNDC collects, evaluates, and disseminates nuclear physics data for basic research and applied nuclear technologies. The NNDC maintains and contributes to the nuclear reaction (ENDF, CSISRS) and nuclear structure databases along with several others databases (CapGam, MIRD, IRDF-2002) and provides coordination for the Cross Section Evaluation Working Group (CSEWG) and the US Nuclear Data Program (USNDP). The Center produces several publications and codes such as Atlas of Neutron Resonances, Nuclear Wallet Cards booklets and develops codes, such as nuclear reaction model code Empire.

PRITYCHENKO, B.; ARCILLA, R.; BURROWS, T.; HERMAN, M.W.; MUGHABGHAB, S.; OBLOZINSKY, P.; ROCHMAN, D.; SONZOGNI, A.A.; TULI, J.; WINCHELL, D.F.

2006-06-05

202

GlycomeDB - integration of open-access carbohydrate structure databases  

PubMed Central

Background Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme for computational purposes. Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. For each database, different encoding schemes for residues and sequence topology were designed. Therefore, it is virtually impossible to obtain an overview of all deposited structures or to compare the contents of the various databases. Results We have implemented procedures which download the structures contained in the seven major databases, e.g. GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). We have created a new database called GlycomeDB, containing all structures, their taxonomic annotations and references (IDs) for the original databases. More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. Inconsistencies were found in all public databases, which were discussed and corrected in multiple feedback rounds with the responsible curators. Conclusion GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. The database is updated weekly and can be downloaded free of charge. The JAVA application GlycoUpdateDB is also available for establishing and updating a local installation of GlycomeDB. With the advent of GlycomeDB, the distributed islands of knowledge in glycomics are now bridged to form a single resource.

Ranzinger, Rene; Herget, Stephan; Wetter, Thomas; von der Lieth, Claus-Wilhelm

2008-01-01

203

Raman Spectroscopy Databases | Spectra Databases  

NSDL National Science Digital Library

This site is a clearinghouse of vibrational frequencies and Raman, mass, fluorescence, neutron scattering and infrared spectra. Both organic and mineral databases are included. The site features free access from both university and industry sources.

Spectroscopynow.com

204

Alcohol Industry & Policy Database  

NSDL National Science Digital Library

The Marin Institute for the Prevention of Alcohol and Other Drug Problems maintains the Alcohol Industry & Policy Database, which contains bibliographic citations and abstracts for more than 13,000 articles and news stories on the alcohol beverage industry, alcohol policy, and the prevention of alcohol-related problems. The citations in the database span from 1991 to the present and are updated monthly. Users may conduct cross-field queries of the database by keywords, subject headings, company name, and publication date. The search facility includes Word Wheels, which are interactive Java applets that help users to identify indexed terms quickly, thereby "eliminat[ing] trial-and-error searching [and] produc[ing] more accurate searches."

Problems., Marin I.

205

National Tourism Database  

NSDL National Science Digital Library

Developed by the Michigan State University Extension Tourism Area of Expertise and the National Tourism Education Design Team, this site contains information on numerous resources related to tourism education, including bulletins, research reports, videos, and training programs. Nearly 100 of the documents featured are full-text. Users can browse the database by topic or browse or search by keyword. A separate list of the full-text publications is also provided. A useful site for students and professionals in the tourism industry.

206

Universal primers for HBV genome DNA amplification across subtypes: a case study for designing more effective viral primers  

Microsoft Academic Search

BACKGROUND: The highly heterogenic characteristic of viruses is the major obstacle to efficient DNA amplification. Taking advantage of the large number of virus DNA sequences in public databases to select conserved sites for primer design is an optimal way to tackle the difficulties in virus genome amplification. RESULTS: Here we use hepatitis B virus as an example to introduce a

Qingrun Zhang; Guanghua Wu; Elliott Richards; Shan'gang Jia; Changqing Zeng

2007-01-01

207

ProtNA-ASA: Protein-nucleic acid structural database with information on accessible surface area  

NASA Astrophysics Data System (ADS)

The article describes a new database (ProtNA-ASA), which combines the data on conformational parameters of nucleic acids and calculations of the accessible surface area (ASA) of nucleic acid atoms in protein-DNA/RNA complexes. As for October 2008, the database contains 214 DNA-protein and 28 RNA-protein non-homologous complexes. The database provides structural parameters that describe local geometry of base pairs and base-pair steps as well as backbone torsion angles. Additionally, total ASA of DNA/RNA atoms and the accessible area of atoms in the minor and major grooves are calculated. ProtNA-ASA database facilitates studying the relationship between the DNA/RNA conformation and availability of atoms for contact with proteins either in major or in minor groove for different nucleotides. Such an analysis is important for understanding the principles of molecular recognition including indirect sequence readout. The database is publicly available for use at http://www.protna.bio-page.org.

Tkachenko, M. Y.; Boryskina, O. P.; Shestopalova, A. V.; Tolstorukov, M. Y.

208

Database Auditing  

Microsoft Academic Search

Government regulations and increased awareness of security issues have increased the auditing requirements of information technology systems. In this paper, we will discuss three government regulations and how they have impacted information technology systems. We classify database auditing systems by considering features of the basic components of an auditing system as proposed by Bishop: the logger, analyzer, and notifier. In

Jungha Woo; Sael Lee; Carla Zoltowski

209

MetaBase--the wiki-database of biological databases  

PubMed Central

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.

Bolser, Dan M.; Chibon, Pierre-Yves; Palopoli, Nicolas; Gong, Sungsam; Jacob, Daniel; Angel, Victoria Dominguez Del; Swan, Dan; Bassi, Sebastian; Gonzalez, Virginia; Suravajhala, Prashanth; Hwang, Seungwoo; Romano, Paolo; Edwards, Rob; Bishop, Bryan; Eargle, John; Shtatland, Timur; Provart, Nicholas J.; Clements, Dave; Renfro, Daniel P.; Bhak, Daeui; Bhak, Jong

2012-01-01

210

Health service use in families where children enter public care: a nested case control study using the General Practice Research Database  

PubMed Central

Background At least 3% of children spend some of their childhood in public care and, as a group, have poor outcomes across a range of education, employment, health and social care outcomes. Research, using social care or government datasets, has identified a number of risk factors associated with children entering public care but the utility of risk factors in clinical practice is not established. This paper uses routine primary health care data to see if risk factors for children entering public care can be identified in clinical practice. Methods A nested case control methodology using routine primary care data from the United Kingdom. Health service use data were extracted for the 12 months before the case child entered public care and compared with 12 months of data for four control mother child pairs per case pair, matched on the age and sex of the child and the general practice. Exposures of interest were developed from a systematic review of the literature on risk factors associated with children entering public care. Results Conditional logistic regression was used to investigate the combined effect of more than one exposure of interest. Maternal mental illness (OR 2.51, 95% CI 1.55-4.05), maternal age at birth of the child, socio-economic status (5th quintile vs. 1st quintile OR 7.14, 95% CI 2.92-17.4), maternal drug use (OR 28.8, 95% CI 2.29-363), non attendance at appointments (OR 2.42, 95% CI 1.42-4.14), child mental illness (OR 2.65, 95% CI 1.42-4.96) and child admission to hospital (OR 3.31, 95% CI 1.21-9.02) were all significantly associated with children entering public care. Maternal use of primary care contraception services was negatively associated with children entering public care (OR 0.52, 95% CI 0.31-0.87). Conclusions Differences in health service use can be identified from routine primary care data in mother child pairs where children enter public care after controlling for maternal age and socio-economic status. The interaction between different risk factors needs testing in a cumulative risk model using longitudinal datasets.

2012-01-01

211

Trail Database  

NSDL National Science Digital Library

Something of a veteran by Internet standards, the Trail Database has been around since 1997 and, as such, now bills itself as the "world's largest hiking trail database." "Henk," the Dutch hiker responsible for this compendium, updates the site regularly and has included a wide variety of links to helpful material here. Users can search or browse the resources, which are arranged both under general topics, such as Knots or Equipment, and by country. Those planning European hikes will find the links off the front page to foot and mouth disease-related hiking restrictions useful (though we found some of these links to be broken). In all, an impressive collection of material. The site is available in Dutch or English.

1997-01-01

212

Publication Bias in Antipsychotic Trials: An Analysis of Efficacy Comparing the Published Literature to the US Food and Drug Administration Database  

PubMed Central

Background Publication bias compromises the validity of evidence-based medicine, yet a growing body of research shows that this problem is widespread. Efficacy data from drug regulatory agencies, e.g., the US Food and Drug Administration (FDA), can serve as a benchmark or control against which data in journal articles can be checked. Thus one may determine whether publication bias is present and quantify the extent to which it inflates apparent drug efficacy. Methods and Findings FDA Drug Approval Packages for eight second-generation antipsychotics—aripiprazole, iloperidone, olanzapine, paliperidone, quetiapine, risperidone, risperidone long-acting injection (risperidone LAI), and ziprasidone—were used to identify a cohort of 24 FDA-registered premarketing trials. The results of these trials according to the FDA were compared with the results conveyed in corresponding journal articles. The relationship between study outcome and publication status was examined, and effect sizes derived from the two data sources were compared. Among the 24 FDA-registered trials, four (17%) were unpublished. Of these, three failed to show that the study drug had a statistical advantage over placebo, and one showed the study drug was statistically inferior to the active comparator. Among the 20 published trials, the five that were not positive, according to the FDA, showed some evidence of outcome reporting bias. However, the association between trial outcome and publication status did not reach statistical significance. Further, the apparent increase in the effect size point estimate due to publication bias was modest (8%) and not statistically significant. On the other hand, the effect size for unpublished trials (0.23, 95% confidence interval 0.07 to 0.39) was less than half that for the published trials (0.47, 95% confidence interval 0.40 to 0.54), a difference that was significant. Conclusions The magnitude of publication bias found for antipsychotics was less than that found previously for antidepressants, possibly because antipsychotics demonstrate superiority to placebo more consistently. Without increased access to regulatory agency data, publication bias will continue to blur distinctions between effective and ineffective drugs. Please see later in the article for the Editors' Summary

Turner, Erick H.; Knoepflmacher, Daniel; Shapley, Lee

2012-01-01

213

American Mineralogist Crystal Structure Database  

NSDL National Science Digital Library

This database provides access to information on every crystal structure published in the American Mineralogist, the Canadian Mineralogist, European Journal of Mineralogy, and Physics and Chemistry of Minerals, as well as selected datasets from other journals. The data are searchable by mineral name, author, chemistry, cell parameters and symmetry, diffraction pattern, and a general search. There are also lists of minerals represented in the database and authors of publications cited.

Downs, R. T.; Hall-Wallace, M.

214

The EMBL Nucleotide Sequence Database  

Microsoft Academic Search

The EMBL Nucleotide Sequence Database (http:\\/\\/ www.ebi.ac.uk\\/embl), maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK, is a comprehensive collection of nucleotide sequences and annotation from available public sources. The database is part of an international collaboration with DDBJ (Japan) and GenBank (USA). Data are exchanged daily between the collaborating institutes toachieveswiftsynchrony.Webinisthepreferredtool for individual submissions of nucleotide sequences, including

Carola Kanz; Philippe Aldebert; Nicola Althorpe; Wendy Baker; Alastair Baldwin; Kirsty Bates; Paul Browne; Alexandra Van Den Broek; Matias Castro; Guy Cochrane; Karyn Duggan; Ruth Eberhardt; Nadeem Faruque; John Gamble; Federico Garcia Diez; Nicola Harte; Tamara Kulikova; Quan Lin; Vincent Lombard; Rodrigo Lopez; Renato Mancuso; Michelle Mchale; Francesco Nardone; Ville Silventoinen; Siamak Sobhany; Peter Stoehr; Mary Ann Tuli; Katerina Tzouvara; Robert Vaughan; Dan Wu; Weimin Zhu; Rolf Apweiler

2005-01-01

215

Visual Exploration of Biomedical Databases  

Microsoft Academic Search

In recent years the amount of public biomedical data has increased dramatically. Improving understanding of these vast, ever-growing repositories of information through visual methods is thus increas- ingly important for biomedical research. A new approach is of- fered for visualizing a query-based subset of the National Center for Biotechnology Information's databases. These databases are modeled as an entity-relation graph, and

Mike Lieberman; Sima Taheri; Inbal Yahav

216

Avibase: The World Bird Database  

NSDL National Science Digital Library

This database provides information on all birds of the world, featuring information on thousands of species and subspecies of birds such as taxonomy, names and synonyms in various languages, photos, distribution maps, and links to additional information from other websites. The database is searchable by keyword or term, exact name, language, year of publication, and other parameters. There is also a search by taxonomic family, a set of checklists by geographic region, and a blog for ornithological discussions.

Lepage, Denis

217

ATIDB: Arabidopsis thaliana insertion database  

Microsoft Academic Search

Insertional mutagenesis techniques, including transposon- and T-DNA-mediated mutagenesis, are key resources for systematic identification of gene function in the model plant species Arabidopsis thaliana. We have developed a database (http:\\/\\/ atidb.cshl.org\\/) for archiving, searching and analyz- ing insertional mutagenesis lines. Flanking sequences from approximately 10 500 insertion lines (including transposon and T-DNA insertions) from several tagging programs in Arabidopsis were

Xiaokang Pan; Hong Liu; Jonathan Clarke; Jonathan Jones; Mike Bevan; Lincoln Stein

2003-01-01

218

The Exoplanet Orbit Database  

NASA Astrophysics Data System (ADS)

We present a database of well-determined orbital parameters of exoplanets, and their host stars' properties. This database comprises spectroscopic orbital elements measured for 427 planets orbiting 363 stars from radial velocity and transit measurements as reported in the literature. We have also compiled fundamental transit parameters, stellar parameters, and the method used for the planets discovery. This Exoplanet Orbit Database includes all planets with robust, well measured orbital parameters reported in peer-reviewed articles. The database is available in a searchable, filterable, and sortable form online through the Exoplanets Data Explorer table, and the data can be plotted and explored through the Exoplanet Data Explorer plotter. We use the Data Explorer to generate publication-ready plots, giving three examples of the signatures of exoplanet migration and dynamical evolution: We illustrate the character of the apparent correlation between mass and period in exoplanet orbits, the different selection biases between radial velocity and transit surveys, and that the multiplanet systems show a distinct semimajor-axis distribution from apparently singleton systems.

Wright, J. T.; Fakhouri, O.; Marcy, G. W.; Han, E.; Feng, Y.; Johnson, John Asher; Howard, A. W.; Fischer, D. A.; Valenti, J. A.; Anderson, J.; Piskunov, N.

2011-04-01

219

Arabidopsis database and stock resources.  

PubMed

The volume of Arabidopsis information has increased enormously in recent years as a result of the sequencing of the reference genome and other large-scale functional genomics projects. Much of the data is stored in public databases, where data are organized, analyzed, and made freely accessible to the research community. These databases are resources that researchers can utilize for making predictions and developing testable hypotheses. The methods in this chapter describe ways to access and utilize Arabidopsis data and genomic resources found in databases and stock centers. PMID:24057361

Li, Donghui; Dreher, Kate; Knee, Emma; Brkljacic, Jelena; Grotewold, Erich; Berardini, Tanya Z; Lamesch, Philippe; Garcia-Hernandez, Margarita; Reiser, Leonore; Huala, Eva

2014-01-01

220

DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs  

Microsoft Academic Search

Although the information of cDNAs is indispensable for analyzing gene function, most of the cDNA sequences stored in current databases are imperfect in the sense that they lack the precise information of 5' end termini. To overcome this difficulty, we have developed the oligo-capping method to obtain full- length cDNAs, the information of which has been partly deposited in public

Yutaka Suzuki; Riu Yamashita; Kenta Nakai; Sumio Sugano

2002-01-01

221

INTEGRALL: a database and search engine for integrons, integrases and gene cassettes.  

PubMed

INTEGRALL is a freely available, text-based search system developed with the aim of collecting and organizing information on integrons in a single database. The current release (1.2) contains more than 4800 integron sequences and provides a public genetic repository for sequence data and nomenclature, offering scientists an easy and interactive access to integron's DNA sequences, their molecular arrangements as well as their genetic contexts. PMID:19228805

Moura, Alexandra; Soares, Mário; Pereira, Carolina; Leitão, Nuno; Henriques, Isabel; Correia, António

2009-02-19

222

The co-occurrence of AIDS and homelessness: results from the integration of administrative databases for AIDS surveillance and public shelter utilisation in Philadelphia  

Microsoft Academic Search

Study objective—Administrative data- bases from the City of Philadelphia that track public shelter utilisation (n=44 337) and AIDS case reporting (n=7749) were merged to identify rates and risk factors for co-occurring homelessness and AIDS. Design—Multiple decrement life tables analyses were conducted, and logistic regression analyses used to identify risk factors associated with AIDS among the homeless, and homelessness among peo-

D P Culhane; E Gollub; R Kuhn; M Shpaner

2008-01-01

223

RWC Music Database: Classical Music Database and Jazz Music Database  

Microsoft Academic Search

This paper describes the design policy and overview ofRWC music database that gives researchers freedom of common use and research use. Various commonly available databases have been built in other research fields because ofthe importance and significance ofthose databases. In the field ofmusical inf ormation processing, however, there has not been any commonly available music database. We have therefore built

Masataka Goto; Hiroki Hashiguchi; Takuichi Nishimura; Ryuichi Oka

2002-01-01

224

ARTI Refrigerant Database  

SciTech Connect

The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air- conditioning and refrigeration equipment. The database identifies sources of specific information on R-32, R-123, R-124, R-125, R-134, R-134a, R-141b, R-142b, R-143a, R-152a, R-245ca, R-290 (propane), R- 717 (ammonia), ethers, and others as well as azeotropic and zeotropic and zeotropic blends of these fluids. It addresses lubricants including alkylbenzene, polyalkylene glycol, ester, and other synthetics as well as mineral oils. It also references documents on compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. A computerized version is available that includes retrieval software.

Calm, J.M.

1992-11-09

225

Searching bibliographic databases for literature on chronic disease and work participation  

Microsoft Academic Search

Results The number of relevant publications retrieved from each database varied. Most (84%) of the relevant publications that were retrieved from each database were unique to that source. For each database, specific search terms for the concept of 'work' were useful for retrieving relevant publications. Conclusion Medline, EMBASE and PsycINFO are useful databases for quick searches. Useful search terms for

Joke Haafkens; Clara Moerman; Merel Schuring; Dijk van F. J. H

2006-01-01

226

Scientists Report New Online Cancer Research Databases  

Cancer.gov

Like the old saying "art for art's sake," most medical researchers once believed that creating large computer databases of known genes or DNA sequences was a case of gathering information for the sake of gathering information.

227

Database systems for knowledge-based discovery.  

PubMed

Several database systems have been developed to provide valuable information from the bench chemist to biologist, medical practitioner to pharmaceutical scientist in a structured format. The advent of information technology and computational power enhanced the ability to access large volumes of data in the form of a database where one could do compilation, searching, archiving, analysis, and finally knowledge derivation. Although, data are of variable types the tools used for database creation, searching and retrieval are similar. GVK BIO has been developing databases from publicly available scientific literature in specific areas like medicinal chemistry, clinical research, and mechanism-based toxicity so that the structured databases containing vast data could be used in several areas of research. These databases were classified as reference centric or compound centric depending on the way the database systems were designed. Integration of these databases with knowledge derivation tools would enhance the value of these systems toward better drug design and discovery. PMID:19727614

Jagarlapudi, Sarma A R P; Kishan, K V Radha

2009-01-01

228

Pyramid Servings Database  

Cancer.gov

Skip to Content Cancer Control and Population Sciences Home Applied Research Home Risk Factor Monitoring and Methods Home Pyramid Servings Database for NHANES III: Pyramid Servings Database Home Accessing the Databases Search the Database Documentation Related

229

NASA Scientific and Technical Publications: A Catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers, 1991-1992.  

National Technical Information Service (NTIS)

This catalog lists 458 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA Scientific and Technical Information database during accession year 199...

1993-01-01

230

NASA Scientific and Technical Publications: A Catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers, 1989.  

National Technical Information Service (NTIS)

This catalog lists 190 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered into the NASA scientific and technical information database during accession year 198...

1990-01-01

231

Virtual Database Technology for Distributed Database  

Microsoft Academic Search

In this paper, our research objective is to develop a database virtualization technique so that data analysts or other users who apply data mining methods to their jobs can use all ubiquitous databases in the Internet as if they were recognized as a single database, thereby helping to reduce their workloads such as data collection from the Internet databases and

Yuji Wada; Yuta Watanabe; Keisuke Syoubu; Jun Sawamoto; Takashi Katoh

2010-01-01

232

NBRP databases: databases of biological resources in Japan  

PubMed Central

The National BioResource Project (NBRP) is a Japanese project that aims to establish a system for collecting, preserving and providing bioresources for use as experimental materials for life science research. It is promoted by 27 core resource facilities, each concerned with a particular group of organisms, and by one information center. The NBRP database is a product of this project. Thirty databases and an integrated database-retrieval system (BioResource World: BRW) have been created and made available through the NBRP home page (http://www.nbrp.jp). The 30 independent databases have individual features which directly reflect the data maintained by each resource facility. The BRW is designed for users who need to search across several resources without moving from one database to another. BRW provides access to a collection of 4.5-million records on bioresources including wild species, inbred lines, mutants, genetically engineered lines, DNA clones and so on. BRW supports summary browsing, keyword searching, and searching by DNA sequences or gene ontology. The results of searches provide links to online requests for distribution of research materials. A circulation system allows users to submit details of papers published on research conducted using NBRP resources.

Yamazaki, Yukiko; Akashi, Ryo; Banno, Yutaka; Endo, Takashi; Ezura, Hiroshi; Fukami-Kobayashi, Kaoru; Inaba, Kazuo; Isa, Tadashi; Kamei, Katsuhiko; Kasai, Fumie; Kobayashi, Masatomo; Kurata, Nori; Kusaba, Makoto; Matuzawa, Tetsuro; Mitani, Shohei; Nakamura, Taro; Nakamura, Yukio; Nakatsuji, Norio; Naruse, Kiyoshi; Niki, Hironori; Nitasaka, Eiji; Obata, Yuichi; Okamoto, Hitoshi; Okuma, Moriya; Sato, Kazuhiro; Serikawa, Tadao; Shiroishi, Toshihiko; Sugawara, Hideaki; Urushibara, Hideko; Yamamoto, Masatoshi; Yaoita, Yoshio; Yoshiki, Atsushi; Kohara, Yuji

2010-01-01

233

ARTI refrigerant database  

SciTech Connect

The Refrigerant Database is an information system on alternative refrigerants, associated lubricants, and their use in air conditioning and refrigeration. It consolidates and facilitates access to property, compatibility, environmental, safety, application and other information. It provides corresponding information on older refrigerants, to assist manufacturers and those using alterative refrigerants, to make comparisons and determine differences. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern. The database provides bibliographic citations and abstracts for publications that may be useful in research and design of air-conditioning and refrigeration equipment. The complete documents are not included, though some may be added at a later date. The database identifies sources of specific information on various refrigerants. It addresses lubricants including alkylbenzene, polyalkylene glycol, polyolester, and other synthetics as well as mineral oils. It also references documents addressing compatibility of refrigerants and lubricants with metals, plastics, elastomers, motor insulation, and other materials used in refrigerant circuits. Incomplete citations or abstracts are provided for some documents. They are included to accelerate availability of the information and will be completed or replaced in future updates.

Calm, J.M.

1997-02-01

234

Quick and Simple Database for Comparing Toxin Sequence Data.  

National Technical Information Service (NTIS)

We describe a method for using two computer programs, a Word Processor and a Search Program, to create a workable, inexpensive database. With these programs, we created databases for comparing Toxin Sequence data, storing lists of publications and produci...

F. W. Sexton

1990-01-01

235

Validation of Toxtree and SciQSAR in silico predictive software using a publicly available benchmark mutagenicity database and their applicability for the qualification of impurities in pharmaceuticals.  

PubMed

The draft ICH M7 guidance (US FDA, 2013) recommends that the computational assessment of bacterial mutagenicity for the qualification of impurities in pharmaceuticals be performed using an expert rule-based method and a second statistically-based (Q)SAR method. The public nonproprietary 6489 compound Hansen benchmark mutagenicity data set was used as an external validation data set for Toxtree, a free expert rule-based SAR software. This is the largest known external validation of Toxtree. The Toxtree external validation specificity, sensitivity, concordance and false negative rate for this mutagenicity data set was 66%, 80%, 74% and 20%, respectively. This mutagenicity data set was also used to create a statistically-based SciQSAR-Hansen mutagenicity model. In a 10% leave-group-out internal cross validation study the specificity, sensitivity, concordance and false negative rate for the SciQSAR mutagenicity model was 71%, 83%, 77% and 17%, respectively. Combining Toxtree and SciQSAR predictions and scoring a positive finding in either software as a positive mutagenicity finding reduced the false negative rate to 7% and increased sensitivity to 93% at the expense of specificity which decreased to 53%. The results of this study support the applicability of Toxtree, and the SciQSAR-Hansen mutagenicity model for the qualification of impurities in pharmaceuticals. PMID:23969001

Contrera, Joseph F

2013-08-19

236

The Molecule Pages database  

PubMed Central

The UCSD-Nature Signaling Gateway Molecule Pages (http://www.signaling-gateway.org/molecule) provides essential information on more than 3800 mammalian proteins involved in cellular signaling. The Molecule Pages contain expert-authored and peer-reviewed information based on the published literature, complemented by regularly updated information derived from public data source references and sequence analysis. The expert-authored data includes both a full-text review about the molecule, with citations, and highly structured data for bioinformatics interrogation, including information on protein interactions and states, transitions between states and protein function. The expert-authored pages are anonymously peer reviewed by the Nature Publishing Group. The Molecule Pages data is present in an object-relational database format and is freely accessible to the authors, the reviewers and the public from a web browser that serves as a presentation layer. The Molecule Pages are supported by several applications that along with the database and the interfaces form a multi-tier architecture. The Molecule Pages and the Signaling Gateway are routinely accessed by a very large research community.

Saunders, Brian; Lyon, Stephen; Day, Matthew; Riley, Brenda; Chenette, Emily; Subramaniam, Shankar

2008-01-01

237

Mouse Phenome Database (MPD)  

PubMed Central

The Mouse Phenome Project was launched a decade ago to complement mouse genome sequencing efforts by promoting new phenotyping initiatives under standardized conditions and collecting the data in a central public database, the Mouse Phenome Database (MPD; http://phenome.jax.org). MPD houses a wealth of strain characteristics data to facilitate the use of the laboratory mouse in translational research for human health and disease, helping alleviate problems involving experimentation in humans that cannot be done practically or ethically. Data sets are voluntarily contributed by researchers from a variety of institutions and settings, or in some cases, retrieved by MPD staff from public sources. MPD maintains a growing collection of standardized reference data that assists investigators in selecting mouse strains for research applications; houses treatment/control data for drug studies and other interventions; offers a standardized platform for discovering genotype–phenotype relationships; and provides tools for hypothesis testing. MPD improvements and updates since our last NAR report are presented, including the addition of new tools and features to facilitate navigation and data mining as well as the acquisition of new data (phenotypic, genotypic and gene expression).

Maddatu, Terry P.; Grubb, Stephen C.; Bult, Carol J.; Bogue, Molly A.

2012-01-01

238

A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity  

EPA Science Inventory

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

239

Cloning and characterisation of a cDNA encoding the Trypanosoma brucei ribosomal protein L24 1 Note: Nucleotide sequence data reported in this paper are available in the GenBank, EMBL, and DDBJ databases under the accession number AF011787. 1  

Microsoft Academic Search

A cDNA encoding ribosomal protein L24 was amplified by PCR from the protozoan parasite, Trypanosoma brucei. The 621 nucleotide cDNA had an open reading frame of 375 nucleotides, predicting a highly basic protein of 125 aa. Database searches revealed 33–40% identity between the T. brucei RPL24 protein and several eukaryotic RPL24 homologues. Southern blot analysis indicated that the gene was

Laurie K Read; Kevin T Militello; George E Nerantzakis

1999-01-01

240

Proposal for a High Energy Nuclear Database.  

National Technical Information Service (NTIS)

We propose to develop a high-energy heavy-ion experimental database and make it accessible to the scientific community through an on-line interface. This database will be searchable and cross-indexed with relevant publications, including published detecto...

D. A. Brown R. Vogt

2005-01-01

241

Correlates of Access to Business Research Databases  

ERIC Educational Resources Information Center

|This study examines potential correlates of business research database access through academic libraries serving top business programs in the United States. Results indicate that greater access to research databases is related to enrollment in graduate business programs, but not to overall enrollment or status as a public or private institution.…

Gottfried, John C.

2010-01-01

242

Mouse Resource Browser--a database of mouse databases.  

PubMed

The laboratory mouse has become the organism of choice for discovering gene function and unravelling pathogenetic mechanisms of human diseases through the application of various functional genomic approaches. The resulting deluge of data has led to the deployment of numerous online resources and the concomitant need for formalized experimental descriptions, data standardization, database interoperability and integration, a need that has yet to be met. We present here the Mouse Resource Browser (MRB), a database of mouse databases that indexes 217 publicly available mouse resources under 22 categories and uses a standardised database description framework (the CASIMIR DDF) to provide information on their controlled vocabularies (ontologies and minimum information standards), and technical information on programmatic access and data availability. Focusing on interoperability and integration, MRB offers automatic generation of downloadable and re-distributable SOAP application-programming interfaces for resources that provide direct database access. MRB aims to provide useful information to both bench scientists, who can easily navigate and find all mouse related resources in one place, and bioinformaticians, who will be provided with interoperable resources containing data which can be mined and integrated. Database URL: http://bioit.fleming.gr/mrb. PMID:20627861

Zouberakis, Michael; Chandras, Christina; Swertz, Morris; Smedley, Damian; Gruenberger, Michael; Bard, Jonathan; Schughart, Klaus; Rosenthal, Nadia; Hancock, John M; Schofield, Paul N; Kollias, George; Aidinis, Vassilis

2010-07-06

243

dbDEPC: a database of Differentially Expressed Proteins in human Cancers  

PubMed Central

Cancer-related investigations have long been in the limelight of biomedical research. Years of effort from scientists and doctors worldwide have generated large amounts of data at the genome, transcriptome, proteome and even metabolome level, and DNA and RNA cancer signature databases have been established. Here we present a database of differentially expressed proteins in human cancers (dbDEPC), with the goal of collecting curated cancer proteomics data, providing a resource for information on protein-level expression changes, and exploring protein profile differences among different cancers. dbDEPC currently contains 1803 proteins differentially expressed in 15 cancers, curated from 65 mass spectrometry (MS) experiments in peer-reviewed publications. In addition to MS experiments, low-throughput experiment data from the same literatures and cancer-associated genes from external databases were also integrated to provide some validation information. Furthermore, dbDEPC associates differential proteins with important structural variations in the human genome, such as copy number variations or single nucleotide polymorphisms, which might be helpful for explaining changes in protein expression at the DNA level. Data in dbDEPC can be queried by protein identifier, description or sequence; the retrieved protein entry provides the differential expression pattern seen in cancers, along with detailed annotations. dbDEPC is expected to be a reference database for cancer signatures at the protein level. This database is provided at http://dbdepc.biosino.org/index/.

Li, Hong; He, Ying; Ding, Guohui; Wang, Chuan; Xie, Lu; Li, Yixue

2010-01-01

244

Accessing Databases from Esterel  

Microsoft Academic Search

A current limitation in reactive systems design is the lack of database support in tools such as Esterel Studio. This report proposes a way of inte- grating databases and Esterel by providing an Application Programming Interface (API) for relational database use inside Esterel. As databases and Esterel programs are often executed on dieren t ma- chines, result sets from database

David White

245

VoSeq: A Voucher and DNA Sequence Web Application  

PubMed Central

There is an ever growing number of molecular phylogenetic studies published, due to, in part, the advent of new techniques that allow cheap and quick DNA sequencing. Hence, the demand for relational databases with which to manage and annotate the amassing DNA sequences, genes, voucher specimens and associated biological data is increasing. In addition, a user-friendly interface is necessary for easy integration and management of the data stored in the database back-end. Available databases allow management of a wide variety of biological data. However, most database systems are not specifically constructed with the aim of being an organizational tool for researchers working in phylogenetic inference. We here report a new software facilitating easy management of voucher and sequence data, consisting of a relational database as back-end for a graphic user interface accessed via a web browser. The application, VoSeq, includes tools for creating molecular datasets of DNA or amino acid sequences ready to be used in commonly used phylogenetic software such as RAxML, TNT, MrBayes and PAUP, as well as for creating tables ready for publishing. It also has inbuilt BLAST capabilities against all DNA sequences stored in VoSeq as well as sequences in NCBI GenBank. By using mash-ups and calls to web services, VoSeq allows easy integration with public services such as Yahoo! Maps, Flickr, Encyclopedia of Life (EOL) and GBIF (by generating data-dumps that can be processed with GBIF's Integrated Publishing Toolkit).

Pena, Carlos; Malm, Tobias

2012-01-01

246

CD-ROM-aided Databases  

NASA Astrophysics Data System (ADS)

CD-ROM has rapidly evolved as a new information medium with large capacity, In the U.S. it is predicted that it will become two hundred billion yen market in three years, and thus CD-ROM is strategic target of database industry. Here in Japan the movement toward its commercialization has been active since this year. Shall CD-ROM bussiness ever conquer information market as an on-disk database or electronic publication? Referring to some cases of the applications in the U.S. the author views marketability and the future trend of this new optical disk medium.

Masuyama, Keiichi

247

Environment Australia's Online Image Database  

NSDL National Science Digital Library

Environment Australia -- Australia's Department of Environment and Heritage -- has made its extensive collection of photographs freely available for non-commercial use. Researchers and students in the environmental sciences may find this collection of well-composed, high-quality images a useful resource for presentations and publications. Users may easily search the database by keyword, general subject, and/or geographic area. Search results yield a table of thumbnail photos together with summary information for each image. Before publishing an image from the database, users must first contact Environment Australia (via provided Web form).

248

Image Databases Are Not Databases with Images  

Microsoft Academic Search

In this paper, we discuss a number of new problems that arise in image databases, and that set them apart from traditional databases. The fact that image databases are based on similarity, rather than match- ing, creates a whose set of new issues.Most noticeably, while matching is, by and large, a well dened concept, there are many possible types of

Simone Santini; Ramesh Jain

1997-01-01

249

Characteristics of Scientific Databases.  

National Technical Information Service (NTIS)

The purpose of this paper is to examine the kinds of data and usage of scientific databases and to identify common characteristics among the different disciplines. Most scientific databases do not use general purpose database management systems (DBMSs). T...

A. Shoshani F. Olken H. K. T. Wong

1984-01-01

250

Generation and Analysis of a Large-Scale Expressed Sequence Tag Database from a Full-Length Enriched cDNA Library of Developing Leaves of Gossypium hirsutum L  

PubMed Central

Background Cotton (Gossypium hirsutum L.) is one of the world’s most economically-important crops. However, its entire genome has not been sequenced, and limited resources are available in GenBank for understanding the molecular mechanisms underlying leaf development and senescence. Methodology/Principal Findings In this study, 9,874 high-quality ESTs were generated from a normalized, full-length cDNA library derived from pooled RNA isolated from throughout leaf development during the plant blooming stage. After clustering and assembly of these ESTs, 5,191 unique sequences, representative 1,652 contigs and 3,539 singletons, were obtained. The average unique sequence length was 682 bp. Annotation of these unique sequences revealed that 84.4% showed significant homology to sequences in the NCBI non-redundant protein database, and 57.3% had significant hits to known proteins in the Swiss-Prot database. Comparative analysis indicated that our library added 2,400 ESTs and 991 unique sequences to those known for cotton. The unigenes were functionally characterized by gene ontology annotation. We identified 1,339 and 200 unigenes as potential leaf senescence-related genes and transcription factors, respectively. Moreover, nine genes related to leaf senescence and eleven MYB transcription factors were randomly selected for quantitative real-time PCR (qRT-PCR), which revealed that these genes were regulated differentially during senescence. The qRT-PCR for three GhYLSs revealed that these genes express express preferentially in senescent leaves. Conclusions/Significance These EST resources will provide valuable sequence information for gene expression profiling analyses and functional genomics studies to elucidate their roles, as well as for studying the mechanisms of leaf development and senescence in cotton and discovering candidate genes related to important agronomic traits of cotton. These data will also facilitate future whole-genome sequence assembly and annotation in G. hirsutum and comparative genomics among Gossypium species.

Pang, Chaoyou; Fan, Shuli; Song, Meizhen; Yu, Shuxun

2013-01-01

251

Database resources for proteomics-based analysis of cancer.  

PubMed

Biological/bioinformatics databases are essential for medical and biological studies. They integrate and organize biologically related information in a structured format and provide researchers with easy access to a variety of relevant data. This review presents an overview of publicly available databases relevant to proteomics studies in cancer research. They include gene/protein expression databases, gene mutation and single nucleotide polymorphisms databases, tumor antigen databases, protein-protein interaction, and biological pathway databases. Automated information retrieval from these databases enables efficient large-scale proteomics data analysis. PMID:21370076

Zhang, Guang Lan; DeLuca, David S; Brusic, Vladimir

2011-01-01

252

Scientific publications about DNA structure-function and PCR technique in Costa Rica: A historic view (1953-2003)  

Microsoft Academic Search

The spreading of knowledge depends on the access to the information and its immediate use. Models are useful to explain specific phenomena. The scientific community accepts some models in Biology after a peri- od of time, once it has evidence to support it. The model of the structure and function of the DNA proposed by Watson & Crick (1953) was

Federico J. Albertazzi

253

The urologic epithelial stem cell database (UESC) - a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder  

PubMed Central

Background Public databases are crucial for analysis of high-dimensional gene and protein expression data. The Urologic Epithelial Stem Cells (UESC) database is a public database that contains gene and protein information for the major cell types of the prostate, prostate cancer cell lines, and a cancer cell type isolated from a primary tumor. Similarly, such information is available for urinary bladder cell types. Description Two major data types were archived in the database, protein abundance localization data from immunohistochemistry images, and transcript abundance data principally from DNA microarray analysis. Data results were organized in modules that were made to operate independently but built upon a core functionality. Gene array data and immunostaining images for human and mouse prostate and bladder were made available for interrogation. Data analysis capabilities include: (1) CD (cluster designation) cell surface protein data. For each cluster designation molecule, a data summary allows easy retrieval of images (at multiple magnifications). (2) Microarray data. Single gene or batch search can be initiated with Affymetrix Probeset ID, Gene Name, or Accession Number together with options of coalescing probesets and/or replicates. Conclusion Databases are invaluable for biomedical research, and their utility depends on data quality and user friendliness. UESC provides for database queries and tools to examine cell type-specific gene expression (normal vs. cancer), whereas most other databases contain only whole tissue expression datasets. The UESC database provides a valuable tool in the analysis of differential gene expression in prostate cancer genes in cancer progression.

Pascal, Laura E; Deutsch, Eric W; Campbell, David S; Korb, Martin; True, Lawrence D; Liu, Alvin Y

2007-01-01

254

The genome sequence DataBase.  

PubMed

The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated biological and bibliographic information. Several notable changes have occurred in the past year: GSDB stopped accepting data submissions from researchers; ownership of data submitted to GSDB was transferred to GenBank; sequence analysis capabilities were expanded to include Smith-Waterman and Frame Search; and Sequence Viewer became available to Mac users. The content of GSDB remains up-to-date because publicly available data is acquired from the International Nucleotide Sequence Database Collaboration databases (IC) on a nightly basis. This allows GSDB to continue providing researchers with the ability to analyze, query and retrieve nucleotide sequences in the database. GSDB and its related tools are freely accessible from the URL: http://www.ncgr.org PMID:10592174

Harger, C; Chen, G; Farmer, A; Huang, W; Inman, J; Kiphart, D; Schilkey, F; Skupski, M P; Weller, J

2000-01-01

255

The Genome Sequence DataBase  

PubMed Central

The Genome Sequence DataBase (GSDB) is a database of publicly available nucleotide sequences and their associated biological and bibliographic information. Several notable changes have occurred in the past year: GSDB stopped accepting data submissions from researchers; ownership of data submitted to GSDB was transferred to GenBank; sequence analysis capabilities were expanded to include Smith–Waterman and Frame Search; and Sequence Viewer became available to Mac users. The content of GSDB remains up-to-date because publicly available data is acquired from the International Nucleotide Sequence Database Collaboration databases (IC) on a nightly basis. This allows GSDB to continue providing researchers with the ability to analyze, query and retrieve nucleotide sequences in the database. GSDB and its related tools are freely accessible from the URL: http://www.ncgr.org

Harger, C.; Chen, G.; Farmer, A.; Huang, W.; Inman, J.; Kiphart, D.; Schilkey, F.; Skupski, M. P.; Weller, J.

2000-01-01

256

USDA Forest Service Southern Research Station: Publications  

NSDL National Science Digital Library

This database contains publications in support of this group\\'s mission to create the science and technology needed to sustain and enhance southern forest ecosystems and the benefits they provide. The database can be searched by author, title, keyword, date range, and publication origin; publication number; and by the most recent publications added to the database. There are also online versions of Compass, a publication catalog of research products from scientists at SRS.

2007-02-17

257

Alcohol Studies Database  

NSDL National Science Digital Library

Since 1987, staff members at the Rutgers University Center of Alcohol Studies have been collecting citations of documents related to alcohol. Today, they have over 80,000 citations and much of the material is related to research and professional materials that deal with the subject. Additionally, the database contains a small collection of educational and prevention materials designed for use by educators, parents, and public health workers. The site is maintained by the Scholarly Communication Center, the Center of Alcohol Studies, and the Rutgers University Libraries. Visitors to the site can search by subject, or perform a more advanced search as well. The site also includes a "Help" area, which includes information on limiting searches, links to full text, and suggestions on using Boolean techniques.

258

World Database of Happiness  

NSDL National Science Digital Library

The World Database of Happiness, maintained by Professor Ruut Veenhoven of Erasmus University Rotterdam, is a "continuous register of scientific research on subjective appreciation of life." This site contains the Bibliography of Happiness, a collection of over 3,000 scientific publications accessible by author or subject; the Catalog of Happiness in Nations, providing responses from over 1,500 national happiness surveys taken in 93 different countries between 1946 and 1996; the Catalog of Happiness Correlates, which presents the abstracts of correlational research findings from 662 studies worldwide; and finally, the Directory of Happiness Investigators, an international listing of more than 3,300 happiness researchers. Users may freely download the Bibliography or the Catalog of Happiness in Nations as compressed MS Access files (.zip), and download the full text of the Catalog of Correlates in compressed RTF format (.zip).

259

National Geologic Map Database  

NSDL National Science Digital Library

The National Geologic Map Database (NGMDB) is an Internet-based system for query and retrieval of earth-science map information, created as a collaborative effort between the USGS and the Association of American State Geologists. Its functions include providing a catalog of available map information; a data repository; and a source for general information on the nature and intended uses of the various types of earth-science information. The map catalog is a comprehensive, searchable catalog of all geoscience maps of the United States, in paper or digital format. It includes maps published in geological survey formal series and open-file series, maps in books, theses and dissertations, maps published by park associations, scientific societies, and other agencies, as well as publications that do not contain a map but instead provide a geological description of an area (for example, a state park). The geologic-names lexicon (GEOLEX) is a search tool for lithologic and geochronologic unit names. It now contains roughly 90% of the geologic names found in the most recent listing of USGS-approved geologic names. Current mapping activities at 1:24,000- and 1:100,000-scale are listed in the Geologic Mapping in Progress Database. Information on how to find topographic maps and list of geology-related links is also available.

1997-01-01

260

Forensic DNA and bioinformatics  

Microsoft Academic Search

The field of forensic science is increasingly based on biomolecular data and many European countries are establishing forensic databases to store DNA profiles of crime scenes of known offenders and apply DNA testing. The field is boosted by statistical and technological advances such as DNA microarray sequencing, TFT biosensors, machine learning algorithms, in particular Bayesian networks, which provide an effective

Lucia Bianchi; Pietro Liò

2007-01-01

261

Informed decision making about predictive DNA tests: arguments for more public visibility of personal deliberations about the good life  

Microsoft Academic Search

Since its advent, predictive DNA testing has been perceived as a technology that may have considerable impact on the quality\\u000a of people’s life. The decision whether or not to use this technology is up to the individual client. However, to enable well\\u000a considered decision making both the negative as well as the positive freedom of the individual should be supported.

Marianne BoeninkSimone van der Burg; Simone van der Burg

2010-01-01

262

Internet image database: development and implementation.  

PubMed

The widespread acceptance of World Wide Web (WWW) hypermedia protocols allows rapid cross-platform development of database interfaces. Using the WWW as the interface promotes easy integration of databases with other publicly available Internet resources. We present our experience with an image database search program (IDBS) developed on the PC platform using freely available UNIX development tools. The database routines were written in PERL. The image database program provides a familiar user interface to a collection of clinical images stored in digital form, either on local media or on the Internet. The design goals of the project and the strategies used to meet them are presented. The source code and a demonstration database are available on the Internet at http:/(/)www.webmedix.com/idbs. PMID:10168953

Buenting, J E; Spencer, E B; Holmes, D K

1997-01-01

263

Accessing Databases within Esterel  

Microsoft Academic Search

Abstract A current limitation in reactive systems design is the lack of database support in tools such as Esterel Studio This report proposes a way of inte - grating databases and Esterel by providing an Application Programming Interface (API) for relational database use inside Esterel As databases and Esterel programs are often executed on di erent ma - chines, result

David White; Gerald Luettgen

2004-01-01

264

Reflective Database Access Control  

ERIC Educational Resources Information Center

|"Reflective Database Access Control" (RDBAC) is a model in which a database privilege is expressed as a database query itself, rather than as a static privilege contained in an access control list. RDBAC aids the management of database access controls by improving the expressiveness of policies. However, such policies introduce new interactions…

Olson, Lars E.

2009-01-01

265

Bibliography on spatiotemporal databases  

Microsoft Academic Search

Spatial and temporal databases are important and well-established sub-disciplines of database research. Some 350 papers in temporal databases have appeared, authored by almost 300 researchers. The literature on spatial databases is also substantial; the bibliography of Samet's landmark book on spatial data structures lists 823 references.

Khaled K. Al-Taha; Richard Thomas Snodgrass; Michael D. Soo

1993-01-01

266

Human gene mutation database-a biomedical information and research resource.  

PubMed

Although 20 years have elapsed since the first single basepair substitution underlying an inherited disease in humans was characterised at the DNA level, the initiative has only recently been taken to establish central database resources for pathological genetic variants. Disease-associated gene lesions are currently collected and publicised by the Human Gene Mutation Database (HGMD) in Cardiff, locus-specific mutation databases, and to some extent also by the Genome Database (GDB) and Online Mendelian Inheritance in Man (OMIM). To date, HGMD represents the only comprehensive and publicly available database of gene lesions underlying human inherited disease. By July 1999, HGMD contained over 18,000 different mutations from some 900 human genes, the majority being single basepair substitutions. In addition to its potential as an information resource for clinicians and genetic counsellors, HGMD has allowed molecular geneticists to address a variety of biological questions through meta-analysis of the collated data. HGMD also promises to assist research workers in optimising mutation search strategies for a given gene. A questionnaire sent out to, and answered by, the editors of 20 key journals revealed that human genetics journals are increasingly reluctant to publish mutation reports. Electronic data submission and publication facilities are therefore urgently required. The World Wide Web (WWW) provides an excellent medium within which to combine the centralised management of basic mutation data, including rigorous quality control, with the possibility of publishing additional mutation-related information. In response to these needs, HGMD has both instituted a collaboration with Springer-Verlag GmbH, Heidelberg, to potentiate free online submission and electronic publication of human gene mutation data and developed links with the curators of locus-specific mutation databases. PMID:10612821

Krawczak, M; Ball, E V; Fenton, I; Stenson, P D; Abeysinghe, S; Thomas, N; Cooper, D N

2000-01-01

267

Establishment and Application of GIS Database in Neighborhood Renewal  

Microsoft Academic Search

This paper is about the establishment and application of GIS database in neighborhood renewal. It first mines the needed data for database establishment from literature review. Then, the GIS database will be designed for neighborhood renewal, which integrates land use, public and commercial service, road, building, infrastructure, and environment six major variables. Finally, a case of Huangjiadun neighborhood in Wuhan,

Rui Li; Bing He

2009-01-01

268

WEBrary: Putting Your In-House Databases on the Web.  

ERIC Educational Resources Information Center

|The WEBrary(R) databases at the Morton Grove Public Library (Illinois) provide patron-accessible searchable databases, easily available over the library's Web site. Database offerings include the locally maintained Song Collection Index, Obituary Index, Continuations Listings, On-Order files, topical and personalized New Acquisitions files, and…

Justie, Kevin M.

1999-01-01

269

Link Discovery in Graphs Derived from Biological Databases (Research Paper)  

Microsoft Academic Search

Public biological databases contain vast amounts of rich data that can also be used to create and evaluate new biological hypothesis. We propose a method for link discovery in biological databases, i.e., for prediction and evaluation of implicit or previously unknown connections between biological entities and concepts. In our framework, information extracted from available databases is represented as a graph,

Petteri Sevon; Lauri Eronen; Petteri Hintsanen; Kimmo Kulovesi; Hannu Toivonen

270

Managing the ADS Citation Database  

NASA Astrophysics Data System (ADS)

The NASA Astrophysics Data System (ADS) has become the standard tool for searching the literature in the astronomy and astrophysics community. Within the ADS we are now consolidating the article reference catalog. Reference sources come in a variety of data formats. OCR'ed scanned articles (HTML, LaTeX, XML...) from a large number of different publications. We present in this paper new developments allowing the automation of the reference digester through a set of highly configurable, object-oriented, Python/XML applications and tools. We expect the use of these tools to ease the burden of incorporating new publications to the reference databases.

Rey-Bakaikoa, V.; Accomazzi, A.; Eichhorn, G.; Grant, C. S.

271

NASA Scientific and Technical Publications: A Catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers 1987-1990.  

National Technical Information Service (NTIS)

This catalog lists 783 citations of all NASA Special Publications, NASA Reference Publications, and NASA Technical Papers that were entered into the NASA Scientific and Technical Information Database during the accession years 1987 through 1990. The entri...

1991-01-01

272

Working with Databases  

Microsoft Academic Search

\\u000a Drupal depends on a database to function correctly. Inside Drupal, a lightweight database abstraction layer exists between\\u000a your code and the database. In this chapter, you’ll learn about how the database abstraction layer works and how to use it.\\u000a You’ll see how queries can be modified by modules. Then, you’ll look at how to connect to additional databases (such as

John K. VanDyk

273

NPIDB: nucleic acid--protein interaction database  

PubMed Central

The Nucleic acid—Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA–protein and RNA–protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid—Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA–binding protein domains and data on conserved water molecules on the DNA–protein interface.

Kirsanov, Dmitry D.; Zanegina, Olga N.; Aksianov, Evgeniy A.; Spirin, Sergei A.; Karyagina, Anna S.; Alexeevski, Andrei V.

2013-01-01

274

Creating a Serial Database Using Subscription Agency Files  

Microsoft Academic Search

Subscription agency invoice files on diskette can be transferred into standard microcomputer database management packages to provide libraries with a fast low-cost serials database useful for various public or technical service functions and for management decision-making. Specific procedures are detailed for producing such a database using EBSCO Subscription Services invoice diskettes and the PC-File III and dBASE III PLUS database

Susan A. Cady

1988-01-01

275

Distinguishing gorilla mitochondrial sequences from nuclear integrations and PCR recombinants: guidelines for their diagnosis in complex sequence databases.  

PubMed

Nuclear integrations of mitochondrial DNA (Numts) are widespread in many taxa and if left undetected can confound phylogeny interpretation and bias estimates of mitochondrial DNA (mtDNA) diversity. This is particularly true in gorillas, where recent studies suggest multiple integrations of the first hypervariable (HV1) domain of the mitochondrial control region. Problems can also arise through the inadvertent incorporation of artifacts produced by in vitro recombination between sequence types during polymerase chain reaction amplification. This issue has attracted little attention yet could potentially exacerbate errors in databases already contaminated by Numts. Using a set of existing diagnostic tools, this study set out to systematically inventory Numts and PCR recombinants in a gorilla HV1 sequence database and address the degree to which existing public databases are contaminated. Phylogenetic analysis revealed three distinct gorilla HV1 Numt groups (I, II, and III) that could be readily differentiated from mtDNA sequences by Numt-specific diagnostic sites and sequence-based motifs. Several instances of genuine recombination were also identified by a suite of detection methods. The location of putative breakpoints was identified by eye and by likelihood analysis. Findings from this study reveal widespread nuclear contamination of gorilla HV1 GenBank databases and underline the importance of recognizing not only Numts but also PCR recombinant artifacts as potential sources of data contamination. Guidelines for the routine identification of Numts and in vitro recombinants are presented and should prove useful in the detection of similar artifacts in other species mtDNA databases. PMID:17084645

Anthony, Nicola M; Clifford, Stephen L; Bawe-Johnson, Mireille; Abernethy, Kate A; Bruford, Michael W; Wickings, E Jean

2006-09-28

276

NASA (National Aeronautics and Space Administration) Scientific and Technical Publications: A Catalog of Special Publications, Reference Publications, Conference Publications, and Technical Papers, 1987.  

National Technical Information Service (NTIS)

This catalog lists 239 citations of all NASA Special Publications, NASA Reference Publications, NASA Conference Publications, and NASA Technical Papers that were entered in the NASA scientific and technical information database during accession year 1987....

1988-01-01

277

PRIDE: the proteomics identifications database.  

PubMed

The advent of high-throughput proteomics has enabled the identification of ever increasing numbers of proteins. Correspondingly, the number of publications centered on these protein identifications has increased dramatically. With the first results of the HUPO Plasma Proteome Project being analyzed and many other large-scale proteomics projects about to disseminate their data, this trend is not likely to flatten out any time soon. However, the publication mechanism of these identified proteins has lagged behind in technical terms. Often very long lists of identifications are either published directly with the article, resulting in both a voluminous and rather tedious read, or are included on the publisher's website as supplementary information. In either case, these lists are typically only provided as portable document format documents with a custom-made layout, making it practically impossible for computer programs to interpret them, let alone efficiently query them. Here we propose the proteomics identifications (PRIDE) database (http://www.ebi.ac.uk/pride) as a means to finally turn publicly available data into publicly accessible data. PRIDE offers a web-based query interface, a user-friendly data upload facility, and a documented application programming interface for direct computational access. The complete PRIDE database, source code, data, and support tools are freely available for web access or download and local installation. PMID:16041671

Martens, Lennart; Hermjakob, Henning; Jones, Philip; Adamski, Marcin; Taylor, Chris; States, David; Gevaert, Kris; Vandekerckhove, Joël; Apweiler, Rolf

2005-08-01

278

16 CFR 1102.28 - Publication of reports of harm.  

Code of Federal Regulations, 2013 CFR

...AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE Procedural Requirements § 1102...the requirements for publication in the Database. The Commission will publish reports...requirements of § 1102.10(d) in the Database beyond the 10-business-day time...

2013-01-01

279

THE ECOTOX DATABASE  

EPA Science Inventory

The database provides chemical-specific toxicity information for aquatic life, terrestrial plants, and terrestrial wildlife. ECOTOX is a comprehensive ecotoxicology database and is therefore essential for providing and suppoirting high quality models needed to estimate population...

280

Sandia Shock Compression Database.  

National Technical Information Service (NTIS)

An authoritative, updatable, and searchable bibliographic database whose topical area is shock compression is currently under development. The database is derived from published scientific articles and reports with current emphasis in the subareas of stre...

C. E. Anderson D. E. Grady J. C. Hokanson J. R. Asay J. S. Wilbeck

1985-01-01

281

Scientific Numeric Databases.  

National Technical Information Service (NTIS)

Scientific numeric databases (SND) are powerful, relatively new research tools for the scientific and technical community. This paper illustrates their use by some practical examples, describes the attributes and capabilities of such databases and gives a...

G. H. Wood

1984-01-01

282

WLN's Database: New Directions.  

ERIC Educational Resources Information Center

|Describes features of the Western Library Network's database, including the database structure, authority control, contents, quality control, and distribution methods. The discussion covers changes in distribution necessitated by increasing telecommunications costs and the development of optical data disk products. (CLB)|

Ziegman, Bruce N.

1988-01-01

283

Databases for LDEF Results.  

National Technical Information Service (NTIS)

One of the objectives of the team supporting the LDEF Systems and Materials Special Investigative Groups is to develop databases of experimental findings. These databases identify the hardware flown, summarize results and conclusions, and provide a system...

G. Bohnhoff-hlavacek

1992-01-01

284

The Organelle Genome Database Project (GOBASE).  

PubMed Central

The taxonomically broad organelle genome database (GOBASE) organizes and integrates diverse data related to organelles (mitochondria and chloroplasts). The current version of GOBASE focuses on the mitochondrial subset of data and contains molecular sequences, RNA secondary structures and genetic maps, as well as taxonomic information for all eukaryotic species represented. The database has been designed so that complex biological queries, especially ones posed in a comparative genomics context, are supported. GOBASE has been implemented as a relational database with a web-based user interface (http://megasun.bch.umontreal.ca/gobase/gobas e.html ). Custom software tools have been written in house to assist in the population of the database, data validation, nomenclature standardization and front-end design. The database is fully operational and publicly accessible via the World Wide Web, allowing interactive browsing, sophisticated searching and easy downloading of data.

Korab-Laskowska, M; Rioux, P; Brossard, N; Littlejohn, T G; Gray, M W; Lang, B F; Burger, G

1998-01-01

285

Overview of biological database mapping services for interoperation between different 'omics' datasets  

PubMed Central

Many primary biological databases are dedicated to providing annotation for a specific type of biological molecule such as a clone, transcript, gene or protein, but often with limited cross-references. Therefore, enhanced mapping is required between these databases to facilitate the correlation of independent experimental datasets. For example, molecular biology experiments conducted on samples (DNA, mRNA or protein) often yield more than one type of 'omics' dataset as an object for analysis (eg a sample can have a genomics as well as proteomics expression dataset available for analysis). Thus, in order to map the two datasets, the identifier type from one dataset is required to be linked to another dataset, so preventing loss of critical information in downstream analysis. This identifier mapping can be performed using identifier converter software relevant to the query and target identifier databases. This review presents the publicly available web-based biological database identifier converters, with comparison of their usage, input and output formats, and the types of available query and target database identifier types.

2011-01-01

286

NIST Special Database 10  

Microsoft Academic Search

This document describes the NIST fingerprint database, NIST Special Database 10. The databaseprovides a large sample of patterns for transitional fingerprint classes and classes with a low naturalfrequency of occurrence in NIST Special Database 9. The 552 fingerprint cards in NIST SpecialDatabase 10 are non-mated cards archived on a set of three CD-ROM's with the first CD-ROMcontaining 2160 fingerprint images

C. I. Watson

1993-01-01

287

Semantics of Database Transformations  

Microsoft Academic Search

. Database transformations arise in many different settings includingdatabase integration, evolution of database systems, and implementing user viewsand data-entry tools. This paper surveys approaches that have been taken to problemsin these settings, assesses their strengths and weaknesses, and develops requirementson a formal model for specifying and implementing database transformations.We also consider the problem of insuring the correctness of database transformations.In

Peter Buneman; Susan B. Davidson; Anthony Kosky

1995-01-01

288

The EPILEPSIAE database: an extensive electroencephalography database of epilepsy patients.  

PubMed

From the very beginning the seizure prediction community faced problems concerning evaluation, standardization, and reproducibility of its studies. One of the main reasons for these shortcomings was the lack of access to high-quality long-term electroencephalography (EEG) data. In this article we present the EPILEPSIAE database, which was made publicly available in 2012. We illustrate its content and scope. The EPILEPSIAE database provides long-term EEG recordings of 275 patients as well as extensive metadata and standardized annotation of the data sets. It will adhere to the current standards in the field of prediction and facilitate reproducibility and comparison of those studies. Beyond seizure prediction, it may also be of considerable benefit for studies focusing on seizure detection, basic neurophysiology, and other fields. PMID:22738131

Klatt, Juliane; Feldwisch-Drentrup, Hinnerk; Ihle, Matthias; Navarro, Vincent; Neufang, Markus; Teixeira, Cesar; Adam, Claude; Valderrama, Mario; Alvarado-Rojas, Catalina; Witon, Adrien; Le Van Quyen, Michel; Sales, Francisco; Dourado, Antonio; Timmer, Jens; Schulze-Bonhage, Andreas; Schelter, Bjoern

2012-06-27

289

Exoplanet Orbit Database (Wright+, 2011)  

NASA Astrophysics Data System (ADS)

We present a database of well determined orbital parameters of exoplanets, and their host stars' properties. This database comprises spectroscopic orbital elements measured for 427 planets orbiting 363 stars from radial velocity and transit measurements as reported in the literature. We have also compiled fundamental transit parameters, stellar parameters, and the method used for the planets discovery. This Exoplanet Orbit Database includes all planets with robust, well measured orbital parameters reported in peer-reviewed articles. The Database is available in a searcheable, filterable, and sortable form on the Web at http://exoplanets.org through the Exoplanets Data Explorer Table, and the data can be plotted and explored through the Exoplanet Data Explorer Plotter. We use the Data Explorer to generate publication-ready plots giving three examples of the signatures of exoplanet migration and dynamical evolution: We illustrate the character of the apparent correlation between mass and period in exoplanet orbits, the different selection biases between radial velocity and transit surveys, and that the multiplanet systems show a distinct semi-major axis distribution from apparently singleton systems. (2 data files).

Wright, J. T.; Kakhouri, O.; Marcy, G. W.; Han, E.; Feng, Y.; Johnson, J. A.; Howard, A. W.; Fischer, D. A.; Valenti, J. A.; Anderson, J.; Piskunov, N.

2013-01-01

290

A database of examples  

Microsoft Academic Search

This report describes the construction of a database of examples of consumer involvement in research. It summarises the material on the accompanying database and discusses some of the problems of finding and classifying suitable examples. The database was commissioned to: map the field of consumer involvement in research, by recording both current and recent initiatives, and the individuals and groups

Paul Dixon; Edwina Peart; Roy Carr-Hill

1999-01-01

291

The Database Layer  

Microsoft Academic Search

\\u000a At its core,Drupal is a tool for creating,maintaining,and displaying information stored in a database. Drupal database management\\u000a is a crucial part of the entire system,as all aspects of a site are stored in the database.

Brian Travis

292

Describing differences between databases  

Microsoft Academic Search

We study the novel problem of efficiently computing the update distance for a pair of relational databases. In analogy to the edit distance of strings, we define the update distance of two databases as the minimal number of insert, delete and modification opera- tions necessary to transform one database into the other. In con- trast to related approaches we consider

Heiko Müller; Johann-Christoph Freytag; Ulf Leser

2006-01-01

293

The Columbia grasp database  

Microsoft Academic Search

Collecting grasp data for learning and bench- marking purposes is very expensive. It would be helpful to have a standard database of graspable objects, along with a set of stable grasps for each object, but no such database exists. In this work we show how to automate the construction of a database consisting of several hands, thousands of objects, and

Corey Goldfeder; Matei T. Ciocarlie; Hao Dang; Peter K. Allen

2009-01-01

294

Silicon Valley Companies Database (SV150)  

NSDL National Science Digital Library

Created by Mercury Center, the online service of the San Jose Mercury News, this database offers financial information and company background for the 150 largest publicly traded companies in Silicon Valley. Silicon Valley is defined as the cities of Santa Cruz and Santa Clara, as well as the southern sections of San Mateo and Alameda counties. The database is searchable by company name, stock symbol, 1997 sales, industry type, product, and location. Clear, detailed instructions will help users best use the database. The search results link to company homepages and charted stock prices.

295

Estimating Haplotype Frequency and Coverage of Databases  

PubMed Central

A variety of forensic, population, and disease studies are based on haploid DNA (e.g. mitochondrial DNA or Y-chromosome data). For any set of genetic markers databases of conventional size will normally contain only a fraction of all haplotypes. For several applications, reliable estimates of haplotype frequencies, the total number of haplotypes and coverage of the database (the probability that the next random haplotype is contained in the database) will be useful. We propose different approaches to the problem based on classical methods as well as new applications of Principal Component Analysis (PCA). We also discuss previous proposals based on saturation curves. Several conclusions can be inferred from simulated and real data. First, classical estimates of the fraction of unseen haplotypes can be seriously biased. Second, there is no obvious way to decide on required sample size based on traditional approaches. Methods based on testing of hypotheses or length of confidence intervals may appear artificial since no single test or parameter stands out as particularly relevant. Rather the coverage may be more relevant since it indicates the percentage of different haplotypes that are contained in a database; if the coverage is low, there is a considerable chance that the next haplotype to be observed does not appear in the database and this indicates that the database needs to be expanded. Finally, freeware and example data sets accompany the methods discussed in this paper: http://folk.uio.no/thoree/nhap/.

Egeland, Thore; Salas, Antonio

2008-01-01

296

Raintree: Tropical Plant Database  

NSDL National Science Digital Library

Hosted by Raintree, the Tropical Plant Database is authored and maintained by Board Certified Naturopath, Ms. Leslie Taylor to provide accurate information about rainforest plants and to help promote rainforest conservation. Including over 300 pages of documentation on rainforest plants and very well-organized, the Tropical Plant Database lists plants by Common name, Botanical name, Ethnic uses, and Action/disorder. The Database File for each plant includes an illustration and information about family, genus, species, common names, plant description, and more. Visitors can link to great illustrations and photos as well as web resources for each plant including Medline Abstracts, W3 TROPICOS Database, Ethnobotany Database, and Phtyochem Database among others. Plant Database File pages include references as well.

297

Resolving database replication conflicts in the health care information system project early phase  

Microsoft Academic Search

Considering that any public health care information system is based on a distributed database management system that consists of many dozens distributed databases, and IS itself can consist of at least few dozens of applications, database replication conflicts can make significant problems to administrators in the system implementing phase. All world known database platforms (like Oracle or SQL Server) have

Tatjana N. Stankovi?; Dragan S. Jankovi?; S. N. Pesic

2009-01-01

298

TOBFAC: the database of tobacco transcription factors  

PubMed Central

Background Regulation of gene expression at the level of transcription is a major control point in many biological processes. Transcription factors (TFs) can activate and/or repress the transcriptional rate of target genes and vascular plant genomes devote approximately 7% of their coding capacity to TFs. Global analysis of TFs has only been performed for three complete higher plant genomes – Arabidopsis (Arabidopsis thaliana), poplar (Populus trichocarpa) and rice (Oryza sativa). Presently, no large-scale analysis of TFs has been made from a member of the Solanaceae, one of the most important families of vascular plants. To fill this void, we have analysed tobacco (Nicotiana tabacum) TFs using a dataset of 1,159,022 gene-space sequence reads (GSRs) obtained by methylation filtering of the tobacco genome. An analytical pipeline was developed to isolate TF sequences from the GSR data set. This involved multiple (typically 10–15) independent searches with different versions of the TF family-defining domain(s) (normally the DNA-binding domain) followed by assembly into contigs and verification. Our analysis revealed that tobacco contains a minimum of 2,513 TFs representing all of the 64 well-characterised plant TF families. The number of TFs in tobacco is higher than previously reported for Arabidopsis and rice. Results TOBFAC: the database of tobacco transcription factors, is an integrative database that provides a portal to sequence and phylogeny data for the identified TFs, together with a large quantity of other data concerning TFs in tobacco. The database contains an individual page dedicated to each of the 64 TF families. These contain background information, domain architecture via Pfam links, a list of all sequences and an assessment of the minimum number of TFs in this family in tobacco. Downloadable phylogenetic trees of the major families are provided along with detailed information on the bioinformatic pipeline that was used to find all family members. TOBFAC also contains EST data, a list of published tobacco TFs and a list of papers concerning tobacco TFs. The sequences and annotation data are stored in relational tables using a PostgrelSQL relational database management system. The data processing and analysis pipelines used the Perl programming language. The web interface was implemented in JavaScript and Perl CGI running on an Apache web server. The computationally intensive data processing and analysis pipelines were run on an Apple XServe cluster with more than 20 nodes. Conclusion TOBFAC is an expandable knowledgebase of tobacco TFs with data currently available for over 2,513 TFs from 64 gene families. TOBFAC integrates available sequence information, phylogenetic analysis, and EST data with published reports on tobacco TF function. The database provides a major resource for the study of gene expression in tobacco and the Solanaceae and helps to fill a current gap in studies of TF families across the plant kingdom. TOBFAC is publicly accessible at .

Rushton, Paul J; Bokowiec, Marta T; Laudeman, Thomas W; Brannock, Jennifer F; Chen, Xianfeng; Timko, Michael P

2008-01-01

299

The Chloroplast Function Database II: a comprehensive collection of homozygous mutants and their phenotypic/genotypic traits for nuclear-encoded chloroplast proteins.  

PubMed

The Chloroplast Function Database has so far offered phenotype information on mutants of the nuclear-encoded chloroplast proteins in Arabidopsis that pertains to >200 phenotypic data sets that were obtained from 1,722 transposon- or T-DNA-tagged lines. Here, we present the development of the second version of the database, which is named the Chloroplast Function Database II and was redesigned to increase the number of mutant characters and new user-friendly tools for data mining and integration. The upgraded database offers information on genome-wide mutant screens for any visible phenotype against 2,495 tagged lines to create a comprehensive homozygous mutant collection. The collection consists of 147 lines with seedling phenotypes and 185 lines for which we could not obtain homozygotes, as well as 1,740 homozygotes with wild-type phenotypes. Besides providing basic information about primer lists that were used for the PCR genotyping of T-DNA-tagged lines and explanations about the preparation of homozygous mutants and phenotype screening, the database includes access to a link between the gene locus and existing publicly available databases. This gives users access to a combined pool of data, enabling them to gain valuable insights into biological processes. In addition, high-resolution images of plastid morphologies of mutants with seedling-specific chloroplast defects as observed with transmission electron microscopy (TEM) are available in the current database. This database is used to compare the phenotypes of visually identifiable mutants with their plastid ultrastructures and to evaluate their potential significance from characteristic patterns of plastid morphology in vivo. Thus, the Chloroplast Function Database II is a useful and comprehensive information resource that can help researchers to connect individual Arabidopsis genes to plastid functions on the basis of phenotype analysis of our tagged mutant collection. It can be freely accessed at http://rarge.psc.riken.jp/chloroplast/. PMID:23230006

Myouga, Fumiyoshi; Akiyama, Kenji; Tomonaga, Yumi; Kato, Aya; Sato, Yuka; Kobayashi, Megumi; Nagata, Noriko; Sakurai, Tetsuya; Shinozaki, Kazuo

2012-12-10

300

The Prostate Expression Database (PEDB): status and enhancements in 2000  

Microsoft Academic Search

The Prostate Expression Database (PEDB) is an online resource designed to access and analyze gene expression information derived from the human prostate. PEDB archives >55 000 expressed sequence tags (ESTs) from 43 cDNA libraries in a curated relational database that provides detailed library information including tissue source, library construction methods, sequence diversity and sequence abundance. The differential expression of each

Peter S. Nelson; Nigel Clegg; Burak Eroglu; Victoria Hawkins; Roger Eugene Bumgarner; Todd Smith; Leroy E. Hood

2000-01-01

301

DNA BARCODING IN LAND PLANTS: DEVELOPING STANDARDS TO QUANTIFY AND MAXIMIZE SUCCESS  

PubMed Central

The selection of a DNA barcode in plants has been impeded in part due to the relatively low rates of nucleotide substitution observed at the most accessible plastid markers. However, the absence of consensus also reflects a lack of standards for comparing potential barcode markers. While many publications have suggested a host of plant DNA barcodes, the studies cannot be readily compared with each other through any quantitative or statistical parameter, partly because they put forward no single compelling rationale relevant to the adoption of a DNA barcode in plants. Here, we argue that the efficacy of any particular plant DNA barcode selection should reflect the anticipated performance of the resulting barcode database in assignment of a query sequence to species. While legitimate scientific disagreement exists over the criteria relevant to “database performance”, the notion gives a unifying rationale for prioritizing selection criteria. Accordingly, we suggest a measure of barcode efficacy based on the rationale of database performance, “the probability of correct identification” (PCI). Moreover, the definition of PCI is left flexible enough to handle most of the scientific disagreement over how to best evaluate DNA barcodes. Finally, we consider how different types of barcodes might require different methods of analysis and database design and indicate how the analysis might affect the selection of the most broadly effective barcode for land plants.

Erickson, David L.; Spouge, John; Resch, Alissa; Weigt, Lee A.; Kress, W. John

2009-01-01

302

Electricity Database Files  

NSDL National Science Digital Library

The Electricity Database Files Web site from the Department of Energy's Energy Information Administration division contains several helpful resources. The site's two main categories are entitled Electric Generator Databases and Power Plant Databases, which contain more than a dozen links to related information. These include everything from an Annual Electric Generator Report, Electric Utilities Database, and a Wholesale Electric Trade Database, to a Clean Air Act Database Browser that provides information about electricity generators that must comply with the sulfur dioxide provisions of the Clean Air Act Amendments of 1990. This unique and informative collection, besides being easy to access, makes utilizing the information simple by allowing users to download the files as either Microsoft Access or Excel files.

303

POW/MIA Database  

NSDL National Science Digital Library

POW/MIA Database. Library of Congress, Washington, D.C.: This database assists researchers investigating the U.S. government documents pertaining to U.S. military personnel killed, missing, or imprisoned in Southeast Asia during or after the American involvement in the Vietnam Conflict. The database is searchable by last name, country name, service branch, or keywords, and copies of desired documents may be obtained from the Library of Congress.

304

The Martian Climate Database  

NSDL National Science Digital Library

This site features access to a database of statistics that was developed in order to describe the climate and surface environment of Mars. The database provides a valuable resource for scientific studies of the Martian atmosphere. The database is based directly on output from multi-annual integrations of two General Circulation Models (GCMs) which were developed jointly at Laboratoire de Météorologie Dynamique du CNRS, Paris, and the University of Oxford, with support from the European Space Agency. The site also includes an online version of a poster that gives examples of database output, including comparisons with previous observations.

Lewis, S. R.; Collins, M.; Read, P. L.; Forget, F.; Fournier, R.; Hourdin, C.

305

Concept for creating in- and preflight databases  

Microsoft Academic Search

In synthetic vision systems (SVS) environmental data and mission critical information must be provided to pilots and system components. For systems with demanding visual graphics representations or enhanced ground proximity warning systems (EGPWS), databases offer data in high resolution with distinct features. Investigations show that pre- and in-flight services and systems such as Aeronautical Publications (AIP), flight planning, map creation,

Jens Schiefele; Ludwig May; Helmut Raabe

1997-01-01

306

The HITRAN 2008 molecular spectroscopic database  

Microsoft Academic Search

This paper describes the status of the 2008 edition of the HITRAN molecular spectroscopic database. The new edition is the first official public release since the 2004 edition, although a number of crucial updates had been made available online since 2004. The HITRAN compilation consists of several components that serve as input for radiative-transfer calculation codes: individual line parameters for

L. S. Rothman; I. E. Gordon; A. Barbe; D. Chris Benner; P. F. Bernath; M. Birk; V. Boudon; L. R. Brown; A. Campargue; J.-P. Champion; K. Chance; L. H. Coudert; V. Dana; V. M. Devi; S. Fally; J.-M. Flaud; R. R. Gamache; A. Goldman; D. Jacquemart; I. Kleiner; N. Lacome; W. J. Lafferty; J.-Y. Mandin; S. T. Massie; S. N. Mikhailenko; C. E. Miller; N. Moazzen-Ahmadi; O. V. Naumenko; A. V. Nikitin; J. Orphal; V. I. Perevalov; A. Perrin; A. Predoi-Cross; C. P. Rinsland; M. Rotger; M. Šime?ková; M. A. H. Smith; K. Sung; S. A. Tashkun; J. Tennyson; R. A. Toth; A. C. Vandaele; J. Vander Auwera

2009-01-01

307

Plant databases and data analysis tools  

Technology Transfer Automated Retrieval System (TEKTRAN)

It is anticipated that the coming years will see the generation of large datasets including diagnostic markers in several plant species with emphasis on crop plants. To use these datasets effectively in any plant breeding program, it is essential to have the information available via public database...

308

Long Valley caldera GIS Database  

NASA Astrophysics Data System (ADS)

In May of 1980, a strong earthquake swarm that included four magnitude 6 earthquakes struck the southern margin of Long Valley Caldera associated with a 25-cm, dome-shaped uplift of the caldera floor. These events marked the onset of the latest period of caldera unrest that continues to this day. This ongoing unrest includes recurring earthquake swarms and continued dome-shaped uplift of the central section of the caldera (the resurgent dome) accompanied by changes in thermal springs and gas emissions. Analysis of combined gravity and geodetic data confirms the intrusion of silicic magma beneath Long Valley caldera. In 1982, the U.S. Geological Survey under the Volcano Hazards Program began an intensive effort to monitor and study geologic unrest in Long Valley Caldera. This database provides an overview of the studies being conducted by the Long Valley Observatory in Eastern California from 1975 to 2000. The database includes geological, monitoring and topographic datasets related to the Long Valley Caldera, plus a number of USGS publications on Long Valley (e.g., fact-sheets, references). Datasets are available as text files or ArcView shapefiles. Database CD-ROM Table of Contents: - Geological data (digital geologic map) - Monitoring data: Deformation (EDM, GPS, Leveling); Earthquakes; Gravity; Hydrologic; CO2 - Topographic data: DEM, DRG, Landsat 7, Rivers, Roads, Water Bodies - ArcView Project File

Williams, M. J.; Battaglia, M.; Hill, D.; Langbein, J.; Segall, P.

2002-12-01

309

High Energy Nuclear Database: A Testbed for Nuclear Data Information Technology.  

National Technical Information Service (NTIS)

We describe the development of an on-line high-energy heavy-ion experimental database. When completed, the database will be searchable and cross-indexed with relevant publications, including published detector descriptions. While this effort is relatively...

B. Beck D. A. Brown J. Pruet R. Vogt

2007-01-01

310

SENTRA, a database of signal transduction proteins.  

SciTech Connect

SENTRA, available via URL http://wit.mcs.anl.gov/WIT2/Sentra/, is a database of proteins associated with microbial signal transduction. The database currently includes the classical two-component signal transduction pathway proteins and methyl-accepting chemotaxis proteins, but will be expanded to also include other classes of signal transduction systems that are modulated by phosphorylation or methylation reactions. Although the majority of database entries are from prokaryotic systems, eukaroytic proteins with bacterial-like signal transduction domains are also included. Currently SENTRA contains signal transduction proteins in 34 complete and almost completely sequenced prokaryotic genomes, as well as sequences from 243 organisms available in public databases (SWISS-PROT and EMBL). The analysis was carried out within the framework of the WIT2 system, which is designed and implemented to support genetic sequence analysis and comparative analysis of sequenced genomes.

D'Souza, M.; Romine, M. F.; Maltsev, N.; Mathematics and Computer Science; PNNL

2000-01-01

311

Physical database design for relational databases  

Microsoft Academic Search

This paper describes the concepts used in the implementation of DBDSGN, an experimental physical design tool for relational databases developed at the IBM San Jose Research Laboratory. Given a workload for System R (consisting of a set of SQL statements and their execution frequencies), DBDSGN suggests physical configurations for efficient performance. Each configuration consists of a set of indices and

Sheldon J. Finkelstein; Mario Schkolnick; Paolo Tiberio

1988-01-01

312

Expression of a novel chickpea Rab-GDI cDNA mainly in seedlings § 1 The nucleotide sequence of the cDNA reported here has been deposited in DDBJ\\/EMBL\\/GenBank DNA databases with the Accession No. AJ005836  

Microsoft Academic Search

Small GTPases of the Rab family are important proteins that take part in the control of vesicular membrane traffic, and the Rab-specific GDP dissociation inhibitor protein is one of the most important accessory proteins that regulate this process. A cDNA clone (CanGDI) encoding a Rab-specific GDP dissociation inhibitor was isolated from a cDNA library from growing epicotyls of Cicer arietinum

Francisco J. Muñoz; Rocío Esteban; Emilia Labrador; Berta Dopico

2001-01-01

313

HGBASE: a database of SNPs and other variations in and around human genes  

PubMed Central

Human genome polymorphism is expected to play a key role in defining the etiologic basis of phenotypic differences between individuals in aspects such as drug responses and common disease predisposition. Relevant functional DNA changes will probably be located in or near to transcribed sequences, and include many single nucleotide polymorphisms. To aid the future analysis of such genome variation, HGBASE (Human Genic Bi-Allelic SEquences) was constructed as a means to gather human gene-linked polymorphisms from all possible public sources, and show these as a non-redundant set of records in a standardized and user-friendly database endowed with text and sequence based search facilities. After 1 year of presence on the WWW, the HGBASE project has compiled data for over 22 000 records, and this number continues to triple every 6–12 months with data harvested or submitted from all major public genome databases and published literature from the previous decade. Extensive annotation enhancement, internal consistency checking and manual review of every record is undertaken to address potential errors and deficiencies sometimes present in the original source data. The fully polished and comprehensive database is made freely available to all at http://hgbase.cgr.ki.se

Brookes, Anthony J.; Lehvaslaiho, Heikki; Siegfried, Marianne; Boehm, Jana G.; Yuan, Yan P.; Sarkar, Chandra M.; Bork, Peer; Ortigao, Flavio

2000-01-01

314

Sandia shock compression database  

Microsoft Academic Search

An authoritative, updatable, and searchable bibliographic database whose topical area is shock compression is currently under development. The database is derived from published scientific articles and reports with current emphasis in the subareas of strength, phase transitions, spall, and stress-volume relations. The content of the cited work is described by keywords which are selected and reviewed by scientific advisors. Keywords

C. E. Anderson; J. S. Wilbeck; J. C. Hokanson; J. R. Asay; D. E. Grady; R. A. Graham; M. E. Kipp

1985-01-01

315

Dictionary as Database.  

ERIC Educational Resources Information Center

|Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)|

Painter, Derrick

1996-01-01

316

Database Searching by Managers.  

ERIC Educational Resources Information Center

|Managers and executives need the easy and quick access to business and management information that online databases can provide, but many have difficulty articulating their search needs to an intermediary. One possible solution would be to encourage managers and their immediate support staff members to search textual databases directly as they…

Arnold, Stephen E.

317

Content Evaluation of Databases.  

ERIC Educational Resources Information Center

Reviews the literature on the content aspects of database quality, specifically scope, composition, currency, accuracy, consistency, completeness, and source, journal, geographic, language, and time-period coverage. These criteria can be evaluated qualitatively and/or quantitatively to determine the profile of a database, and to ascertain search…

Jacso, Peter

1997-01-01

318

Build Your Own Database.  

ERIC Educational Resources Information Center

This book is intended to help librarians and others to produce databases of better value and quality, especially if they have had little previous experience in database construction. Drawing upon almost 40 years of experience in the field of information retrieval, this book emphasizes basic principles and approaches rather than in-depth and…

Jacso, Peter; Lancaster, F. W.

319

Visual Palaeomagnetic Database  

Microsoft Academic Search

The Global Palaeomagnetic Database (GPMDB) created and developed by McElhinny and Lock (1991, 1996) is used by researchers all over the world. The user-friendly interface makes it unnecessary for users to learn about details of the Microsoft Access software. The next step in the development of these databases lies in the visualisation of data and in the integration of the

S. Pisarevsky

2002-01-01

320

Coalescing in Temporal Databases  

Microsoft Academic Search

Coalescing is a unary operator applicable totemporal databases; it is similar to duplicateelimination in conventional databases. Tuplesin a temporal relation that agree on theexplicit attribute values and that have adjacentor overlapping time periods are candidatesfor coalescing. Uncoalesced relationscan arise in many ways, e.g., via a projectionor union operator, or by not enforcing coalescingon update or insertion. In this paperwe show

Michael H. Böhlen; Richard T. Snodgrass; Michael D. Soo

1996-01-01

321

Web Database Development.  

National Technical Information Service (NTIS)

This thesis explores the concept of Web Database Development using Active Server Pages (ASP) and Java Server Pages (JSP). These are among the leading technologies in the web database development. The focus of this thesis was to analyze and compare the ASP...

N. A. Tsardas

2001-01-01

322

Dictionary as Database.  

ERIC Educational Resources Information Center

Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

Painter, Derrick

1996-01-01

323

First Look: TRADEMARKSCAN Database.  

ERIC Educational Resources Information Center

|Describes database produced by Thomson and Thomson and available on Dialog which contains over 700,000 records representing all active federal trademark registrations and applications for registrations filed in United States Patent and Trademark Office. A typical record, special features, database applications, learning to use TRADEMARKSCAN, and…

Fernald, Anne Conway; Davidson, Alan B.

1984-01-01

324

Database Searching by Managers.  

ERIC Educational Resources Information Center

Managers and executives need the easy and quick access to business and management information that online databases can provide, but many have difficulty articulating their search needs to an intermediary. One possible solution would be to encourage managers and their immediate support staff members to search textual databases directly as they now…

Arnold, Stephen E.

325

Designing secure databases  

Microsoft Academic Search

Security is an important issue that must be considered as a fundamental requirement in information systems development, and particularly in database design. Therefore security, as a further quality property of software, must be tackled at all stages of the development. The most extended secure database model is the multilevel model, which permits the classification of information according to its confidentiality,

Eduardo Fernández-medina; Mario Piattini

2005-01-01

326

DNA secret writing techniques  

Microsoft Academic Search

The paper presents the principles of bio molecular computation (BMC) and several algorithms for DNA (deoxyribonucleic acid) steganography and cryptography: One-Time-Pad (OTP), DNA XOR OTP and DNA chromosomes indexing. It represents a synthesis of our work in the field, sustained by former referred publications. Experimental results obtained using Matlab Bioinformatics Toolbox and conclusions are ending the work.

Monica BORDA; Olga TORNEA

2010-01-01

327

Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers  

PubMed Central

Background Most information on genomic variations and their associations with phenotypes are covered exclusively in scientific publications rather than in structured databases. These texts commonly describe variations using natural language; database identifiers are seldom mentioned. This complicates the retrieval of variations, associated articles, as well as information extraction, e. g. the search for biological implications. To overcome these challenges, procedures to map textual mentions of variations to database identifiers need to be developed. Results This article describes a workflow for normalization of variation mentions, i.e. the association of them to unique database identifiers. Common pitfalls in the interpretation of single nucleotide polymorphism (SNP) mentions are highlighted and discussed. The developed normalization procedure achieves a precision of 98.1 % and a recall of 67.5% for unambiguous association of variation mentions with dbSNP identifiers on a text corpus based on 296 MEDLINE abstracts containing 527 mentions of SNPs. The annotated corpus is freely available at http://www.scai.fraunhofer.de/snp-normalization-corpus.html. Conclusions Comparable approaches usually focus on variations mentioned on the protein sequence and neglect problems for other SNP mentions. The results presented here indicate that normalizing SNPs described on DNA level is more difficult than the normalization of SNPs described on protein level. The challenges associated with normalization are exemplified with ambiguities and errors, which occur in this corpus.

2011-01-01

328

FORMIDABEL: The Belgian Ants Database.  

PubMed

FORMIDABEL is a database of Belgian Ants containing more than 27.000 occurrence records. These records originate from collections, field sampling and literature. The database gives information on 76 native and 9 introduced ant species found in Belgium. The collection records originated mainly from the ants collection in Royal Belgian Institute of Natural Sciences (RBINS), the 'Gaspar' Ants collection in Gembloux and the zoological collection of the University of Liège (ULG). The oldest occurrences date back from May 1866, the most recent refer to August 2012. FORMIDABEL is a work in progress and the database is updated twice a year. THE LATEST VERSION OF THE DATASET IS PUBLICLY AND FREELY ACCESSIBLE THROUGH THIS URL: http://ipt.biodiversity.be/resource.do?r=formidabel. The dataset is also retrievable via the GBIF data portal through this link: http://data.gbif.org/datasets/resource/14697 A dedicated geo-portal, developed by the Belgian Biodiversity Platform is accessible at: http://www.formicidae-atlas.be Purpose: FORMIDABEL is a joint cooperation of the Flemish ants working group "Polyergus" (http://formicidae.be) and the Wallonian ants working group "FourmisWalBru" (http://fourmiswalbru.be). The original database was created in 2002 in the context of the preliminary red data book of Flemish Ants (Dekoninck et al. 2003). Later, in 2005, data from the Southern part of Belgium; Wallonia and Brussels were added. In 2012 this dataset was again updated for the creation of the first Belgian Ants Atlas (Figure 1) (Dekoninck et al. 2012). The main purpose of this atlas was to generate maps for all outdoor-living ant species in Belgium using an overlay of the standard Belgian ecoregions. By using this overlay for most species, we can discern a clear and often restricted distribution pattern in Belgium, mainly based on vegetation and soil types. PMID:23794918

Brosens, Dimitri; Vankerkhoven, François; Ignace, David; Wegnez, Philippe; Noé, Nicolas; Heughebaert, André; Bortels, Jeannine; Dekoninck, Wouter

2013-06-03

329

Fire Ecology Database  

NSDL National Science Digital Library

The Tall Timbers Research Station, a research and conservation organization located in Tallahassee, Florida, has recently made available this searchable Fire Ecology Database. International in scope, the database covers a broad range of fire-related information with emphasis on North America, in particular, the southeastern US. Updated continuously, the Fire Ecology Database currently includes citations for nearly 12,000 "references to books, chapters within books, journal articles, conferences and conference papers, state and federal documents," and abstracts. Users may search the database by author, keywords, periodical, year, or title. Typical returns include full citations of related articles. A 40-page downloadable thesaurus accompanies the database and may also be used to assist in keyword searches.

330

VoSeq: a voucher and DNA sequence web application.  

PubMed

There is an ever growing number of molecular phylogenetic studies published, due to, in part, the advent of new techniques that allow cheap and quick DNA sequencing. Hence, the demand for relational databases with which to manage and annotate the amassing DNA sequences, genes, voucher specimens and associated biological data is increasing. In addition, a user-friendly interface is necessary for easy integration and management of the data stored in the database back-end. Available databases allow management of a wide variety of biological data. However, most database systems are not specifically constructed with the aim of being an organizational tool for researchers working in phylogenetic inference. We here report a new software facilitating easy management of voucher and sequence data, consisting of a relational database as back-end for a graphic user interface accessed via a web browser. The application, VoSeq, includes tools for creating molecular datasets of DNA or amino acid sequences ready to be used in commonly used phylogenetic software such as RAxML, TNT, MrBayes and PAUP, as well as for creating tables ready for publishing. It also has inbuilt BLAST capabilities against all DNA sequences stored in VoSeq as well as sequences in NCBI GenBank. By using mash-ups and calls to web services, VoSeq allows easy integration with public services such as Yahoo! Maps, Flickr, Encyclopedia of Life (EOL) and GBIF (by generating data-dumps that can be processed with GBIF's Integrated Publishing Toolkit). PMID:22720030

Peña, Carlos; Malm, Tobias

2012-06-12

331

DOLOP: A Database of Bacterial Lipoproteins  

NSDL National Science Digital Library

Bacteria rely on protein-lipid combinations known as lipoproteins to glom onto surfaces, sense their surroundings, slurp up nutrients, shuttle DNA to other cells, and perform other life tasks. Researchers can analyze more than 270 of the molecules at DOLOP, a database from the Medical Research Council Laboratory of Molecular Biology in Cambridge, U.K. Entries describe each protein, indicate its size and function, and provide links to the Swiss-Prot database, where you can parse the molecule's sequence and structural features. The site also explains the synthesis of lipoproteins and describes the lipobox, a characteristic amino acid string to which lipids attach.

M. Maden Babu (MRC-Laboratory of Molecular Biology, Cambridge;); K. Sankaran (Centre for Biotechnology, Anna University, Chennai ;)

2001-09-15

332

The Vocational Guidance Research Database: A Scientometric Approach  

ERIC Educational Resources Information Center

|The scientometric study of scientific output through publications in specialized journals cannot be undertaken exclusively with the databases available today. For this reason, the objective of this article is to introduce the "Base de Datos de Investigacion en Orientacion Vocacional" [Vocational Guidance Research Database], based on the use of…

Flores-Buils, Raquel; Gil-Beltran, Jose Manuel; Caballer-Miedes, Antonio; Martinez-Martinez, Miguel Angel

2012-01-01

333

Nucleotide sequence databases: a gold mine for biologists  

Microsoft Academic Search

The rapid expansion of nucleotide sequence data available in public databases is revolutionizing biomedical research. These databases have a variety of uses, including the discovery of novel genes, identification of homologous genes, analysis of alternative splicing, chromosomal localization of genes, and detection of polymorphisms. Data sets such as the human transcript map will undoubtedly accelerate identification of candidate genes in

Akhilesh Pandey; Fran Lewitter

1999-01-01

334

Online Information. Selected Databases at the New York State Library.  

ERIC Educational Resources Information Center

This brochure describes the online information services at the New York State Library, which has online access to over 250 databases covering a broad range of subject areas, including current events, law, science, medicine, public affairs, grants, business, computer technology, education, social welfare, and humanities. Many of these databases are…

New York State Library, Albany. Database Services.

335

Canonicalization of database records using adaptive similarity measures  

Microsoft Academic Search

It is becoming increasingly common to construct databases from information automatically culled from many heteroge- neous sources. For example, a research publication database can be constructed by automatically extracting titles, au- thors, and conference information from online papers. A common diculty in consolidating data from multiple sources is that records are referenced in a variety of ways (e.g. ab- breviations,

Aron Culotta; Michael Wick; Robert Hall; Matthew Marzilli; Andrew Mccallum

2007-01-01

336

A catalog of human cDNA expression clones and its application to structural genomics  

Microsoft Academic Search

We describe here a systematic approach to the identification of human proteins and protein fragments that can be expressed as soluble proteins in Escherichia coli. A cDNA expression library of 10,825 clones was screened by small-scale expression and purification and 2,746 clones were identified. Sequence and protein-expression data were entered into a public database. A set of 163 clones was

Konrad Büssow; Claudia Quedenau; Volker Sievert; Janett Tischer; Christoph Scheich; Harald Seitz; Brigitte Hieke; Frank H Niesen; Frank Götz; Ulrich Harttig; Hans Lehrach

2004-01-01

337

A Workload-Driven Unit of Cache Replacement for Mid-Tier Database Caching  

Microsoft Academic Search

Making multi-terabyte scientific databases publicly accessible over the Internet is increasingly important in disciplines such as Biology and Astronomy. However, contention at a centralized, backend database is a major performance bottleneck, limiting the scalability of Internet-based, database applications. Mid- tier caching reduces contention at the backend database by distributing database operations to the cache. To improve the performance of mid-tier

Xiaodan Wang; Tanu Malik; Randal C. Burns; Stratos Papadomanolakis; Anastassia Ailamaki

2007-01-01

338

The Stanford Microarray Database: data access and quality assessment tools.  

PubMed

The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code and providing full public access to data published by SMD users, along with many tools to explore and analyze those data. SMD currently provides public access to data from 3500 microarrays, including data from 85 publications, and this total is increasing rapidly. In this article, we describe some of SMD's newer tools for accessing public data, assessing data quality and for data analysis. PMID:12519956

Gollub, Jeremy; Ball, Catherine A; Binkley, Gail; Demeter, Janos; Finkelstein, David B; Hebert, Joan M; Hernandez-Boussard, Tina; Jin, Heng; Kaloper, Miroslava; Matese, John C; Schroeder, Mark; Brown, Patrick O; Botstein, David; Sherlock, Gavin

2003-01-01

339

The NCBI Taxonomy database  

PubMed Central

The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the sequences represented in the INSDC’s nucleotide and protein sequence databases. The taxonomy database is manually curated by a small group of scientists at the NCBI who use the current taxonomic literature to maintain a phylogenetic taxonomy for the source organisms represented in the sequence databases. The taxonomy database is a central organizing hub for many of the resources at the NCBI, and provides a means for clustering elements within other domains of NCBI web site, for internal linking between domains of the Entrez system and for linking out to taxon-specific external resources on the web. Our primary purpose is to index the domain of sequences as conveniently as possible for our user community.

Federhen, Scott

2012-01-01

340

RRSS Publications- Methodological Issues - Health Status  

Cancer.gov

Skip to Main Content at the National Institutes of Health | www.cancer.gov Home Methodologic Issues Cancer Treatment & Outcomes Monitoring Screening Practices Health Behaviors & Risk Factors Linking Databases Technical Aspects of Registry Operations Publications Publications

341

JICST Factual Database(3)  

NASA Astrophysics Data System (ADS)

This paper describes the system outline, characteristics and use of JICST Thermophysical and Thermochemical Properties Database of which service was started as one part of JICST Factual Database System. This system enables to store data of more than 60 kinds of physical or chemical thermal properties. It covers elements, pure substances of inorganic and low molecular organic compounds, and two or three component systems of these compounds. The system is designed to enable to deal with floating decimal point numerical data identifying significant figures, to provide versatile searching supports, and to link its searching to other databases. The actual use examples and some points to be careful are also described.

Shimura, Kazuki; Abe, Atsushi

342

World Biodiversity Database  

NSDL National Science Digital Library

The World Biodiversity Database, provided by the Expert Center for Taxonomic Identification (ETI), seeks to "document all presently known species (about 1.7 million) and to make this important biological information worldwide accessible." This continually growing database "provides taxonomic information, species names, synonyms, descriptions, illustrations and literature references when available" on 200,000 taxa. The searchable database can be explored using an expandable tree of the five taxonomic kingdoms or by typing in a common or scientific name. Both educators and students should find this site easy to navigate, informative, and useful.

343

Eurodino Database Project  

NSDL National Science Digital Library

Hosted by DinoData, The Eurodino Database Project was developed by paleontologist Octavio Mateus as a service for the European paleontological community. The database is designed to inform professional and amateur paleontologists of the locations of "originals or casts of each dinosaur in each museum in Europe." The database provides several mechanisms to search for dinosaur fossils and museums and allows users to search for fossils alphabetically and through categories such as Eggs, Footprints, Skin, and Coprolites. Additionally, users can search for museums by perusing the comprehensive European museum list or by selecting a specific country. This site is also reviewed in the January 23, 2004 _NSDL Life Sciences Report_.

344

The Mendel Database  

NSDL National Science Digital Library

The Mendel Database, part of the Mendel Plant Gene Nomenclature Database project by the Mendel Bioinformatics Group (UK), "aims to develop a common nomenclature for sequenced genes, based on gene families, for all photosynthetic organisms, the organelle genomes of both photosynthetic and non-photosynthetic organisms (fungi, algae, and protozoa) and plant viruses." At present, the searchable database contains "more than 20,000 genes, which can be translated into proteins, organized into about 2,000 gene families based on their sequence homology." Typical entries include gene family number and gene family name, "Gene & Gene Product descriptions & synonyms, and Accession numbers with links to SWISS-PROT & EMBL."

345

World Cave Database  

NSDL National Science Digital Library

The World Cave Database was created by Eric Madelaine of the French Research Institute for Computer Science and Automatic Control. Users can browse the database by depth, length, or an alphabetical listing of the caves, and can search the nearly 1000 entries by keyword. All included caves are 300 meters deep and 3 kilometers long and larger, including the longest, which is the Mammoth Cave system in the US that is known to be 563,270 meters long. After getting used to the somewhat cryptic layout of cave listings, users should find the database a useful and informative resource.

346

Year 2000 Reports Database  

NSDL National Science Digital Library

The US Securities and Exchange Commission (SEC) has recently released this searchable database of Y2K readiness reports in order to disclose the preparatory efforts of the securities industry. The database contains more than 13,000 reports from the broker-dealers, transfer agents, investment advisors, and mutual funds required to file with the SEC. Reports include descriptions of the company's, agent's, or fund's state of Y2K readiness, costs to address the Y2K problem, Y2K risks, and contingency plans. Complete database documentation, search instructions, and contact information are provided at the Important Information page.

1999-01-01

347

JICST Factual Database(2)  

NASA Astrophysics Data System (ADS)

The computer programme, which builds atom-bond connection tables from nomenclatures, is developed. Chemical substances with their nomenclature and varieties of trivial names or experimental code numbers are inputted. The chemical structures of the database are stereospecifically stored and are able to be searched and displayed according to stereochemistry. Source data are from laws and regulations of Japan, RTECS of US and so on. The database plays a central role within the integrated fact database service of JICST and makes interrelational retrieval possible.

Araki, Keisuke

348

DNA barcoding insect-host plant associations  

PubMed Central

Short-sequence fragments (‘DNA barcodes’) used widely for plant identification and inventorying remain to be applied to complex biological problems. Host–herbivore interactions are fundamental to coevolutionary relationships of a large proportion of species on the Earth, but their study is frequently hampered by limited or unreliable host records. Here we demonstrate that DNA barcodes can greatly improve this situation as they (i) provide a secure identification of host plant species and (ii) establish the authenticity of the trophic association. Host plants of leaf beetles (subfamily Chrysomelinae) from Australia were identified using the chloroplast trnL(UAA) intron as barcode amplified from beetle DNA extracts. Sequence similarity and phylogenetic analyses provided precise identifications of each host species at tribal, generic and specific levels, depending on the available database coverage in various plant lineages. The 76 species of Chrysomelinae included—more than 10 per cent of the known Australian fauna—feed on 13 plant families, with preference for Australian radiations of Myrtaceae (eucalypts) and Fabaceae (acacias). Phylogenetic analysis of beetles shows general conservation of host association but with rare host shifts between distant plant lineages, including a few cases where barcodes supported two phylogenetically distant host plants. The study demonstrates that plant barcoding is already feasible with the current publicly available data. By sequencing plant barcodes directly from DNA extractions made from herbivorous beetles, strong physical evidence for the host association is provided. Thus, molecular identification using short DNA fragments brings together the detection of species and the analysis of their interactions.

Jurado-Rivera, Jose A.; Vogler, Alfried P.; Reid, Chris A.M.; Petitpierre, Eduard; Gomez-Zurita, Jesus

2008-01-01

349

The Thirty Meter Telescope Site Testing Database  

NASA Astrophysics Data System (ADS)

The Thirty Meter Telescope (TMT) site testing campaign was one of the most comprehensive campaigns ever undertaken for the placement of a telescope. The campaign consisted of five candidate sites, each with several instruments placed on the mountain to test various atmospheric and meteorological parameters. The resulting data set is immense. During the site testing campaign, a database was created to manage the data as it was gathered, giving the TMT site testing team the ability to monitor the progress of the campaign and ensure the validity of the data. At the conclusion of the TMT site testing campaign, the database was made public.

Riddle, R.

2011-11-01

350

THE CTEPP DATABASE  

EPA Science Inventory

The CTEPP (Children's Total Exposure to Persistent Pesticides and Other Persistent Organic Pollutants) database contains a wealth of data on children's aggregate exposures to pollutants in their everyday surroundings. Chemical analysis data for the environmental media and ques...

351

The Gymnosperm Database  

NSDL National Science Digital Library

This database is a fabulous resource for students and researchers of conifers, cycads, and their allies; it was created by Dr. Christopher J. Earle, a dendrochronologist and doctorate of the University of Washington. The user enters the taxonomic database at the highest level, Order and Family, and can then navigate to Species (or sometimes Variety) levels. At each level, information on the taxon is provided, along with bibliographic citations. In addition to the gymnosperm database, the site provides a links page with pointers to bibliographic databases, virtual image galleries and other resources. Special sections on gymnosperms of Alta California, gymnosperms of Sichuan, tree age determination, paleobotany of Australia and New Zealand conifers, and podocarp forests of south-west New Zealand further complement the site.

352

Prostate Expression Database.  

National Technical Information Service (NTIS)

This proposal aims to exploit advances in biotechnology and informatics to develop a genetics resource termed the Prostate Expression Database (PEDB) (http://www.pedb.org). The foundation of PEDB is the identification and characterization of a prostate tr...

P. S. Nelson

2001-01-01

353

Dissolution Methods Database  

Center for Drug Evaluation (CDER)

... For a drug product that does not have a dissolution test method in the United States Pharmacopeia (USP), the FDA Dissolution Methods Database ... More results from www.fda.gov/drugs/informationondrugs

354

ARD: Anthropology Review Database  

NSDL National Science Digital Library

The fully searchable and browseable ARD, the Anthropology Review Database, indexes scholarly, reviews of anthropological books, audiovisual materials, exhibits, conferences, software, and online resources. Each query yields a webliography linking users to online reviews.

Jarvis, Hugh W.

355

Freshwater Biological Traits Database.  

National Technical Information Service (NTIS)

The Freshwater Biological Traits Database currently contains traits data for 3,857 North American macroinvertebrate taxa and includes habitat, life history, mobility, morphology, and ecological trait data. Species traits are the characteristics that expla...

2012-01-01

356

ARTI Refrigerant Database  

SciTech Connect

The Refrigerant Database consolidates and facilitates access to information to assist industry in developing equipment using alternative refrigerants. The underlying purpose is to accelerate phase out of chemical compounds of environmental concern.

Calm, J.M. [Calm (James M.), Great Falls, VA (United States)

1994-05-27

357

Database Delivers Contaminant Resources  

EPA Science Inventory

The US Environmental Protection Agency's Drinking Water Treatability Database presents referenced information on the control of contaminants in drinking water. The TDB allows a variety of drinking water professionals to access information gathered from thousands of literature so...

358

TREATABILITY DATABASE DESCRIPTION  

EPA Science Inventory

The Drinking Water Treatability Database (TDB) presents referenced information on the control of contaminants in drinking water. It allows drinking water utilities, first responders to spills or emergencies, treatment process designers, research organizations, academics, regulato...

359

CAL Learning Strategies Database  

NSDL National Science Digital Library

The Learning Strategies Database, developed by the Center for Advancement of Learning (CAL) at Muskingum College, organizes information about learning strategies into four major sections: Introduction to the CAL Learning Strategies Database, General-Purpose Learning Strategies, Content-Specific Learning Strategies, and Bibliography of Learning Strategies Resources. Each section is further divided into more specific subsections, creating a hierarchical database structure. For example, the general-purpose section contains sixteen subsections related to general learning, such as Memory, Test Preparation, and Notetaking; whereas, the content-specific section has 27 disciplinary subsections, covering subjects in the natural sciences, social sciences, humanities, and arts. The information in the database allows students of all ages and their instructors to assess current learning styles, and to identify and implement methods for effective education adapted to the learning strengths and weaknesses of individual students.

360

Spanky Fractal Database  

NSDL National Science Digital Library

Spanky Fractal Database: fractal images, programs, documents, papers, code examples, and other fractal related material. Submitted by contributors or hunted down from various nooks and crannies on the net. Enjoy and discover.

361

Native Health Research Database  

MedlinePLUS

... THIS APP WITH JAVASCRIPT TURNED OFF. THE NATIVE HEALTH DATABASE REQUIRES JAVASCRIPT IN ORDER TO FUNCTION. PLEASE ... Data and Links, U.S. Census Bureau American Indian Health from the National Library of Medicine Arctic Health ...

362

Integrating Database Software.  

National Technical Information Service (NTIS)

This report contains the final version of the Integrated Database (IDB) in Microsoft Access format. The report briefly describes the system architecture, the developmental environment, hardware requirements, supporting software requirements, and installat...

J. A. Briscoe

1997-01-01

363

ECMDB: the E. coli Metabolome Database.  

PubMed

The Escherichia coli Metabolome Database (ECMDB, http://www.ecmdb.ca) is a comprehensively annotated metabolomic database containing detailed information about the metabolome of E. coli (K-12). Modelled closely on the Human and Yeast Metabolome Databases, the ECMDB contains >2600 metabolites with links to ?1500 different genes and proteins, including enzymes and transporters. The information in the ECMDB has been collected from dozens of textbooks, journal articles and electronic databases. Each metabolite entry in the ECMDB contains an average of 75 separate data fields, including comprehensive compound descriptions, names and synonyms, chemical taxonomy, compound structural and physicochemical data, bacterial growth conditions and substrates, reactions, pathway information, enzyme data, gene/protein sequence data and numerous hyperlinks to images, references and other public databases. The ECMDB also includes an extensive collection of intracellular metabolite concentration data compiled from our own work as well as other published metabolomic studies. This information is further supplemented with thousands of fully assigned reference nuclear magnetic resonance and mass spectrometry spectra obtained from pure E. coli metabolites that we (and others) have collected. Extensive searching, relational querying and data browsing tools are also provided that support text, chemical structure, spectral, molecular weight and gene/protein sequence queries. Because of E. coli's importance as a model organism for biologists and as a biofactory for industry, we believe this kind of database could have considerable appeal not only to metabolomics researchers but also to molecular biologists, systems biologists and individuals in the biotechnology industry. PMID:23109553

Guo, An Chi; Jewison, Timothy; Wilson, Michael; Liu, Yifeng; Knox, Craig; Djoumbou, Yannick; Lo, Patrick; Mandal, Rupasri; Krishnamurthy, Ram; Wishart, David S

2012-10-29

364

Complex Carbohydrate Research Center Spectral Databases  

NSDL National Science Digital Library

Dr. William York of the Complex Carbohydrate Research Center has created these two databases with scientific input from others at the University of Georgia. The Xyloglucan NMR Database consists of a searchable table of the ?H-NMR chemical shifts of xyloglucan oligoglycosyl alditols. Xyloglucans are highly branched polymers with a cellulosic backbone (i.e., consisting of b-(1,4)-linked D-glucosyl residues). The basis for the most commonly used nomenclature for xyloglucan structures comes from the linear array of glycosyl side chains that many of the backbone residues bear. The Partially Methylated Alditol Acetate (PMAA) Database shows the molecular structures of PMAAs derived from Hexopyranosyl, Pentopyranosyl, and Pentofuranosyl Residues. Users view the structures by gliding the mouse over a table. The PMAA Database also says that electron-impact mass spectra are available, but at the time of publication, these links weren't working. The Xyloglucan database comes with overviews, search guides, and nomenclature information. The PMAA database has a help page. Both require a free login.

York, William ..

2001-01-01

365

National Plants Database  

NSDL National Science Digital Library

This United States Department of Agriculture (USDA) database is a single source collection of standardized information about plants of the US and its territories. The database includes names, checklists, automated tools, identification information, species abstracts, distributional data, crop information, plant symbols, plant growth data, plant materials information, links to more resources, references, and other facts. A search tool and photo gallery display plants of interest.

366

Chemical Synthesis Database  

NSDL National Science Digital Library

This database provides information on thousands of chemical compounds, including synthesis references and physical properties. The database is searchable by keyword and browseable by journal title. For each compound, the information includes molecular formula and weight, Chemical Abstracts Service (CAS) numbers, International Chemical Identifier (InChIKey), and Simplified Molecular Input Line Entry System (SMILES) notation. There is also information on synonyms, physical properties (boiling and melting points, density), an illustration of chemical structure, spectral data, and links to additional data.

367

ICE Biological Inventories Databases  

NSDL National Science Digital Library

The Information Center for the Environment (ICE) is a cooperative effort between scientists at University of California -- Davis and collaborators from over thirty organizations involved in environmental protection." The ICE Biological Inventory Databases contain "documented, taxonomically standardized species inventories of plants and animals reported from the world's protected areas." New to the Scout Report, these online databases have been updated recently to include botanical inventories from protected areas in Costa Rica and South Africa.

2008-07-08

368

ICE Biological Inventories Databases  

NSDL National Science Digital Library

The Information Center for the Environment (ICE) is a cooperative effort between scientists at University of California -- Davis and collaborators from over thirty organizations involved in environmental protection." The ICE Biological Inventory Databases contain "documented, taxonomically standardized species inventories of plants and animals reported from the world's protected areas." New to the Scout Report, these online databases have been updated recently to include botanical inventories from protected areas in Costa Rica and South Africa.

2000-01-01

369

Ecomp Executive Compensation Database  

NSDL National Science Digital Library

The Ecomp Executive Compensation Database allows users to research the compensation and net-worth of executives. Users may search the database by company name or ticker symbol, as well as by state, sector, and industry pull-down menus. Search returns list compensation summaries for the top executives, including salary, bonus, and total compensation. Clicking on the executive's name will give a more detailed summary, including restricted stock, LTIP payouts, and value realized for options exercised. All numbers are for 1999.

370

ECOTOX Database System  

NSDL National Science Digital Library

The US Environmental Protection Agency (EPA) provides this database of chemical toxicity. Three individual EPA databases are combined to provide information on chemical-specific toxicity values for aquatic and terrestrial plants and animals. Users can search for research reports by chemical name, species name, or environmental effect. The site has informative help files and browse features. This Web site is useful for evaluating industrial chemicals or for environmental assessment research.

2008-09-02

371

ECOTOX Database System  

NSDL National Science Digital Library

The US Environmental Protection Agency (EPA) provides this database of chemical toxicity. Three individual EPA databases are combined to provide information on chemical-specific toxicity values for aquatic and terrestrial plants and animals. Users can search for research reports by chemical name, species name, or environmental effect. The site has informative help files and browse features. This Web site is useful for evaluating industrial chemicals or for environmental assessment research.

2000-01-01

372

West Indian Orchidaceae Database  

NSDL National Science Digital Library

The New York Botanical Garden has recently placed online this searchable database of West Indian Orchids. Containing approximately 5,200 specimen records for the family Orchidacese (from the New York Botanical Garden's collection), the database may be searched by Family, Collector, Country, Taxon, State/Province, and other select fields. Typical returns provide information on Specimen name (scientific name), Location, Collector, Description, and Habitat.

373

Querying genomic databases  

SciTech Connect

A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

1991-09-01

374

Automated Pattern Database Design  

Microsoft Academic Search

Pattern databases are dictionaries for heuristic estimates based on state-to-goal distances in state space abstractions. Their effectiveness is sensitive to the selection of the under- lying patterns. Especially for multiple and additive pattern databases, a manual selection of pattern sets that lead to good exploration results is involved. For automating the selection process, greedy bin-packing strategies have been suggested. This

Stefan Edelkamp

375

JICST Factual Database(4)  

NASA Astrophysics Data System (ADS)

JICST Mass Spectral Database which had started from March, 1987 made a fresh start at January, 1988 as JOIS-F (JICST Online Information System-Fact) including two other JICST Factual Databases. Renewal point of it are data up-dated, a new function of cross-retrieval and a small change of command. The outline of data items, retrieval system and availability are given again.

Okano, Keiko; Abe, Atsushi

376

The HUMAINE Database  

Microsoft Academic Search

\\u000a The HUMAINE Database is grounded in HUMAINE’s core emphasis on considering emotion in a broad sense – ‘pervasive emotion’\\u000a – and engaging with the way it colours action and interaction. The aim of the database is to provide a resource to which the\\u000a community can go to see and hear the forms that emotion takes in everyday action and interaction,

Ellen Douglas-Cowie; Cate Cox; Jean-Claude Martin; Laurence Devillers; Roddy Cowie; Ian Sneddon; Margaret McRorie; Catherine Pelachaud; Christopher Peters; Orla Lowry; Anton Batliner; Florian Hönig

377

Atlas Florae Europaeae Database  

NSDL National Science Digital Library

Initiated in 1992, the primary goal of the Atlas Florae Europaeae (AFE) Database project is to make plant distribution data available in digital format. Currently, AFE includes "preliminary maps for all European vascular plants" (based on the time period 1972-1996), examples of distribution statistics (colorful summary maps), and Biogeographical analyses; digital data are expected in 1999. PC users can download an evaluation copy of the current database (which will be available for sale in 1999) on-site.

1992-01-01

378

Databases: Peter's Picks and Pans.  

ERIC Educational Resources Information Center

Reviews the best and worst in databases on disk, CD-ROM, and online, and offers judgments and observations on database characteristics. Two databases are praised and three are criticized. (Author/JMV)

Jacso, Peter

1995-01-01

379

Lies, Damned Lies, and Databases.  

National Technical Information Service (NTIS)

A database is usually expected to give correct and complete answers to queries. However, some applications take confidentiality to an extreme and require the database to receive some users by supplying incorrect answers. In most secure databases classifyi...

S. Wiseman

1991-01-01

380

The comprehensive peptaibiotics database.  

PubMed

Peptaibiotics are nonribosomally biosynthesized peptides, which - according to definition - contain the marker amino acid ?-aminoisobutyric acid (Aib) and possess antibiotic properties. Being known since 1958, a constantly increasing number of peptaibiotics have been described and investigated with a particular emphasis on hypocrealean fungi. Starting from the existing online 'Peptaibol Database', first published in 1997, an exhaustive literature survey of all known peptaibiotics was carried out and resulted in a list of 1043 peptaibiotics. The gathered information was compiled and used to create the new 'The Comprehensive Peptaibiotics Database', which is presented here. The database was devised as a software tool based on Microsoft (MS) Access. It is freely available from the internet at http://peptaibiotics-database.boku.ac.at and can easily be installed and operated on any computer offering a Windows XP/7 environment. It provides useful information on characteristic properties of the peptaibiotics included such as peptide category, group name of the microheterogeneous mixture to which the peptide belongs, amino acid sequence, sequence length, producing fungus, peptide subfamily, molecular formula, and monoisotopic mass. All these characteristics can be used and combined for automated search within the database, which makes The Comprehensive Peptaibiotics Database a versatile tool for the retrieval of valuable information about peptaibiotics. Sequence data have been considered as to December 14, 2012. PMID:23681723

Stoppacher, Norbert; Neumann, Nora K N; Burgstaller, Lukas; Zeilinger, Susanne; Degenkolb, Thomas; Brückner, Hans; Schuhmacher, Rainer

2013-05-01

381

Open systems and databases  

SciTech Connect

This paper is part of a series of papers invited by the IEEE POWER CONTROL CENTER WORKING GROUP concerning the changing designs of modern control centers. Papers invited by the Working Group discuss the following issues: Benefits of Openness, Criteria for Evaluating Open EMS Systems, Hardware Design, Configuration Management, Security, Project Management, Databases, SCADA, Inter- and Intra-System Communications and Man-Machine Interfaces,'' The goal of this paper is to provide an introduction to the issues pertaining to Open Systems and Databases.'' The intent is to assist understanding of some of the underlying factors that effect choices that must be made when selecting a database system for use in a control room environment. This paper describes and compares the major database information models which are in common use for database systems and provides an overview of SQL. A case for the control center community to follow the workings of the non-formal standards bodies is presented along with possible uses and the benefits of commercially available databases within the control center. The reasons behind the emergence of industry supported standards organizations such as the Open Software Foundation (OSF) and SQL Access are presented.

Martire, G.S. (ECC, Inc., Fairfax, VA (United States)); Nuttall, D.J.H. (Unified Information, Inc., Kirkland, WA (United States))

1993-05-01

382

The PROSITE database, its status in 2002  

Microsoft Academic Search

PROSITE (Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583-3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215-219) is a method of identifying the functions of uncharacterized proteins translated from genomic or cDNA sequences. The PROSITE database (http:\\/\\/www.expasy.org\\/prosite\\/) consists of biologically significant patterns and profiles designed in such a way that with appropriate compu- tational tools it can rapidly

Laurent Falquet; Marco Pagni; Philipp Bucher; Nicolas Hulo; Christian J. A. Sigrist; Kay Hofmann; Amos Bairoch

2002-01-01

383

Illinois State Archives: Database of Illinois Civil War Veterans  

NSDL National Science Digital Library

This database from the Illinois State Archives "indexes the first eight volumes of the nine volume publication, Report of the Adjutant General of the State of Illinois." The publication is drawn from the original rosters maintained during the Civil War by the Adjutant General. In addition to the names of approximately 250,000 men organized into 175 regiments, this searchable database also provides histories of the Illinois units and regiments. The database was created and donated to the Illinois State Archives by amateur genealogist Fred Delap of Kansas, Illinois.

384

Three Decades of Recombinant DNA.  

ERIC Educational Resources Information Center

|Discusses highlights in the development of genetic engineering, examining techniques with recombinant DNA, legal and ethical issues, GenBank (a national database of nucleic acid sequences), and other topics. (JN)|

Palmer, Jackie

1985-01-01

385

Local and Regional Funding Mechanisms for Public Transportation.  

National Technical Information Service (NTIS)

TCRP Report 129: Local and Regional Funding Mechanisms for Public Transportation and the Local and Regional Funding Database will be of interest to public transportation systems, local and regional governments, and others interested in funding for public ...

K. Stouffer

2005-01-01

386

On the Probability of Matching DNA Fingerprints  

Microsoft Academic Search

Forensic scientists commonly assume that DNA fingerprint patterns are infrequent in the general population and that genotypes are independent across loci. To test these assumptions, the number of matching DNA patterns in two large databases from the Federal Bureau of Investigation (FBI) and from Lifecodes was determined. No deviation from independence across loci in either database was apparent. For the

Neil J. Risch; B. Devlin

1992-01-01

387

Great Basin paleontological database  

USGS Publications Warehouse

The U.S. Geological Survey has constructed a paleontological database for the Great Basin physiographic province that can be served over the World Wide Web for data entry, queries, displays, and retrievals. It is similar to the web-database solution that we constructed for Alaskan paleontological data (www.alaskafossil.org). The first phase of this effort was to compile a paleontological bibliography for Nevada and portions of adjacent states in the Great Basin that has recently been completed. In addition, we are also compiling paleontological reports (Known as E&R reports) of the U.S. Geological Survey, which are another extensive source of l,egacy data for this region. Initial population of the database benefited from a recently published conodont data set and is otherwise focused on Devonian and Mississippian localities because strata of this age host important sedimentary exhalative (sedex) Au, Zn, and barite resources and enormons Carlin-type An deposits. In addition, these strata are the most important petroleum source rocks in the region, and record the transition from extension to contraction associated with the Antler orogeny, the Alamo meteorite impact, and biotic crises associated with global oceanic anoxic events. The finished product will provide an invaluable tool for future geologic mapping, paleontological research, and mineral resource investigations in the Great Basin, making paleontological data acquired over nearly the past 150 yr readily available over the World Wide Web. A description of the structure of the database and the web interface developed for this effort are provided herein. This database is being used ws a model for a National Paleontological Database (which we am currently developing for the U.S. Geological Survey) as well as for other paleontological databases now being developed in other parts of the globe. ?? 2008 Geological Society of America.

Zhang, N.; Blodgett, R. B.; Hofstra, A. H.

2008-01-01

388

Chemical Explosion Database  

NASA Astrophysics Data System (ADS)

A database containing information on chemical explosions, recorded and located by the International Data Center (IDC) of the CTBTO, should be established in the IDC prior to entry into force of the CTBT. Nearly all of the large chemical explosions occur in connection with mining activity. As a first step towards the establishment of this database, a survey of presumed mining areas where sufficiently large explosions are conducted has been done. This is dominated by the large coal mining areas like the Powder River (U.S.), Kuznetsk (Russia), Bowen (Australia) and Ekibastuz (Kazakhstan) basins. There are also several other smaller mining areas, in e.g. Scandinavia, Poland, Kazakhstan and Australia, with large enough explosions for detection. Events in the Reviewed Event Bulletin (REB) of the IDC that are located in or close to these mining areas, and which therefore are candidates for inclusion in the database, have been investigated. Comparison with a database of infrasound events has been done as many mining blasts generate strong infrasound signals and therefore also are included in the infrasound database. Currently there are 66 such REB events in 18 mining areas in the infrasound database. On a yearly basis several hundreds of events in mining areas have been recorded and included in the REB. Establishment of the database of chemical explosions requires confirmation and ground truth information from the States Parties regarding these events. For an explosion reported in the REB, the appropriate authority in whose country the explosion occurred is encouraged, on a voluntary basis, to seek out information on the explosion and communicate this information to the IDC.

Johansson, Peder; Brachet, Nicolas

2010-05-01

389

CD-ROM-aided Databases  

NASA Astrophysics Data System (ADS)

CD-ROM is remarked as an epoch-making medium because of its advantages such as large capacity, compact size, mass reproducibility, read only memory and cost performance ratio. Some of big dictionaries and online databases have been converted to CD-ROM versions so far, however, information of publication or machine parts are converted recently. Moreover various CD-ROM-aided products such as support system for R&D, decision making and so on are being turned out. Still there remain many problems on sophisticated utilization of CD-ROM and distributive machinery of information. Author reviews this mini-series and describes the prospects of development of CD-ROM.

Fujiwara, Yuzuru

390

MPW : the metabolic pathways database.  

SciTech Connect

The Metabolic Pathways Database (MPW) (www.biobase.com/emphome.html/homepage. html.pags/pathways.html) a derivative of EMP (www.biobase.com/EMP) plays a fundamental role in the technology of metabolic reconstructions from sequenced genomes under the PUMA (www.mcs.anl.gov/home/compbio/PUMA/Production/ ReconstructedMetabolism/reconstruction.html), WIT (www.mcs.anl.gov/home/compbio/WIT/wit.html ) and WIT2 (beauty.isdn.msc.anl.gov/WIT2.pub/CGI/user.cgi) systems. In October 1997, it included some 2800 pathway diagrams covering primary and secondary metabolism, membrane transport, signal transduction pathways, intracellular traffic, translation and transcription. In the current public release of MPW (beauty.isdn.mcs.anl.gov/MPW), the encoding is based on the logical structure of the pathways and is represented by the objects commonly used in electronic circuit design. This facilitates drawing and editing the diagrams and makes possible automation of the basic simulation operations such as deriving stoichiometric matrices, rate laws, and, ultimately, dynamic models of metabolic pathways. Individual pathway diagrams, automatically derived from the original ASCII records, are stored as SGML instances supplemented by relational indices. An auxiliary database of compound names and structures, encoded in the SMILES format, is maintained to unambiguously connect the pathways to the chemical structures of their intermediates.

Selkov, E., Jr.; Grechkin, Y.; Mikhailova, N.; Selkov, E.; Mathematics and Computer Science; Russian Academy of Sciences

1998-01-01

391

The BAX Database (Blanchard+, 2004)  

NASA Astrophysics Data System (ADS)

We present BAX, Base de Donnees Amas de Galaxies X (http://bax.ast.obs-mip.fr), a multi-wavelength database dedicated to X-ray clusters and groups of galaxies allowing detailed information retrieval. BAX is designed to support astronomical research by providing access to published measurements of the main physical quantities and to the related bibliographic references: basic data stored in the database are cluster/group identifiers, equatorial coordinates, redshift, flux, X-ray luminosity (in the ROSAT band) and temperature, and links to additional linked parameters (in X-rays, such as spatial profile parameters, as well as SZ parameters of the hot gas, lensing measurements, and data at other wavelengths, such as optical and radio). The clusters and groups in BAX can be queried by the basic parameters as well as the linked parameters or combinations of these. We expect BAX to become an important tool for the astronomical community. BAX will optimize various aspects of the scientific analysis of X-ray clusters and groups of galaxies, from proposal planning to data collection, interpretation and publication, from both ground based facilities like MEGACAM (CFHT), VIRMOS (VLT) and space missions like XMM-Newton, Chandra and Planck. (1 data file).

Sadat, R.; Blanchard, A.; Kneib, J.-P.; Mathez, G.; Madore, B.; Mazzarella, J. M.

2004-08-01

392

SCMD: Saccharomyces cerevisiae Morphological Database  

PubMed Central

To study the global regulation of cell morphology, a number of groups have recently reported genome-wide screening data for yeast mutants with abnormal morphology. Despite the relatively simple ellipsoidal shape of yeast cells, in the past, cell morphology researchers have processed information on cells manually. These time-consuming, entirely subjective tasks motivated us to develop image-processing software that automatically extracts yeast cells from micrographs and processes them to measure key morphological characteristics such as cell size, roundness, bud neck position angle, nuclear DNA localization and actin localization. To date, we have retrieved 960 609 cells from 52 988 micrographs of 2531 mutants using our software, and we have published the results in the Saccharomyces cerevisiae Morphological Database (SCMD), which facilitates the analysis of abnormal cells. Our system provides quantitative data for shapes of the daughter and mother cells, localization of the nuclear DNA and morphology of the actin patches. To search for mutants with similar morphological traits, the system outputs a list of mutants ranked by similarity of average morphological parameters. The SCMD is available at http://yeast.gi.k.u-tokyo.ac.jp/.

Saito, Taro L.; Ohtani, Miwaka; Sawai, Hiroshi; Sano, Fumi; Saka, Ayaka; Watanabe, Daisuke; Yukawa, Masashi; Ohya, Yoshikazu; Morishita, Shinichi

2004-01-01

393

National Hazards Center HazLit Database  

NSDL National Science Digital Library

HazLit is the on-line library database of the Natural Hazards Research and Applications Information Center at the University of Colorado at Boulder. The Hazards Center Library contains a large collection (approximately 17,000 items) of social science literature focusing on how society prepares for, responds to, recovers from, and mitigates natural disasters. Approximately one-third of the collection is fully annotated in the database. The Hazards Center Library is a nonlending library, but researchers planning a trip or ordering documents through their local library can use this site to identify publications of interest. In addition to the database, the site offers general information on the library and its custom search service.

394

Role of exposure databases in risk management  

SciTech Connect

Despite the development of numerous national exposure-related databases, exposure assessment remains a weak link in the chain of risk assessment and risk-management activities. Most databases include measures of environmental releases or concentrations of pollutants in specific media, but do not include actual measures of exposure. If accurate estimates of exposure experienced by populations or individuals are absent, it is impossible to judge the effectiveness of risk-management strategies. The Risk Management Work Group evaluation identified the following needs: refinement of measurements of total exposure experienced by individuals, improved characterization of the distribution of exposures in the population, longitudinal monitoring of exposure trends, and improved information about the public health implications of exposure. Recommendations are presented with the hope that the utility of existing databases will be improved and that future initiatives will be developed that meet the needs of risk management.

Burke, T.; Anderson, H.; Beach, N.; Colome, S.; Drew, R.T.; Firestone, M.; Hauchman, F.S.; Miller, T.O.; Wagener, D.K.; Zeise, L. (Johns Hopkins Univ., Baltimore, MD (United States))

1992-11-01

395

gender Inn: Women's and Gender Studies Database  

NSDL National Science Digital Library

This searchable bibliographic database contains records describing over 5,000 works on "feminist theory, feminist literary criticism and gender studies focusing on English and American literature" from 1950 to the present. The search form is available under the heading Research, where users may indicate which field to search, limit by year of publication, and specify whether to return results in English or German. Works included in the database have been assigned up to 20 keywords from a locally-developed thesaurus for feminist research. A German version of the thesaurus is available in the Deutsche (German) Version and work is underway to translate the thesaurus into English. Work on this database was started in 1987 by Professor Natasha Wurzbach of the University of Cologne (Germany) English Department, and was made accessible via the Internet through a cooperative project with the Department of Art and Design at the Fachhochschule Koln.

1997-01-01

396

Rice Annotation Database (RAD): a contig-oriented database for map-based rice genomics.  

PubMed

A contig-oriented database for annotation of the rice genome has been constructed to facilitate map-based rice genomics. The Rice Annotation Database has the following functional features: (i) extensive effort of manual annotations of P1-derived artificial chromosome/bacterial artificial chromosome clones can be merged at chromosome and contig-level; (ii) concise visualization of the annotation information such as the predicted genes, results of various prediction programs (RiceHMM, Genscan, Genscan+, Fgenesh, GeneMark, etc.), homology to expressed sequence tag, full-length cDNA and protein; (iii) user-friendly clone / gene query system; (iv) download functions for nucleotide, amino acid and coding sequences; (v) analysis of various features of the genome (GC-content, average value, etc.); and (vi) genome-wide homology search (BLAST) of contig- and chromosome-level genome sequence to allow comparative analysis with the genome sequence of other organisms. As of October 2004, the database contains a total of 215 Mb sequence with relevant annotation results including 30 000 manually curated genes. The database can provide the latest information on manual annotation as well as a comprehensive structural analysis of various features of the rice genome. The database can be accessed at http://rad.dna.affrc.go.jp/. PMID:15608281

Ito, Yuichi; Arikawa, Kohji; Antonio, Baltazar A; Ohta, Isamu; Naito, Shinji; Mukai, Yoshiyuki; Shimano, Atsuko; Masukawa, Masatoshi; Shibata, Michie; Yamamoto, Mayu; Ito, Yukiyo; Yokoyama, Junri; Sakai, Yasumichi; Sakata, Katsumi; Nagamura, Yoshiaki; Namiki, Nobukazu; Matsumoto, Takashi; Higo, Kenichi; Sasaki, Takuji

2005-01-01

397

Global Invasive Species Database  

NSDL National Science Digital Library

The Global Invasive Species Database was developed by the Invasive Species Specialist Group (ISSG), an international group of 100+ scientific and policy experts with the Species Survival Commission (SSC) of the International Union for the Conservation of Nature (IUCN). The entry page of the Website offers background information on invasive species and instructions on how to use the database. A section entitled 100 of the worst (ranging from Rat to Purple Loosestrife) gives viewers an idea of the type of information that will be included in the database, both in terms of expected detail and organizational structure of the database. Types of information provided for each species include Ecology, Distribution, Habitat Matches, References, and Contacts. In addition, a Predictive feature allows viewers to predict the expansion of invasive species, and the Early Warning System matches habitats that the species has already invaded with "other similar habitats around the world." Although still under construction, this database should be a powerful tool for researchers and educators, once completed.

398

Distributed database schema  

NASA Astrophysics Data System (ADS)

The Science Data Processing System (SDPS) application, described herein as an example, has had a long development cycle. The SDPS application incorporates IDL, C++, and Perl programming languages, with significant use of an Oracle Relational Database Management System (RDBMS). The time involved from initial design, 1996, to operational deployment, on July 15th, 2004, with the launch of the Aura spacecraft, spans several releases of the Oracle RDBMS. New database versions usher in new features and performance enhancements, sometimes requiring modifications to custom application code to take full advantage of improvements in technology. For a project with an aggressive release schedule, major redesigns of the custom code could jeopardize the successful completion of mission criteria. Over time, higher throughput requirements and hardware improvements in the application computing infrastructure revealed database performance bottlenecks due to increased scanning frequency of ever-growing tables and indexes. The Distributed Schema (DS) database redesign successfully addressed the database scalability and performance limitations, with only minor SIPS application changes and no changes to the TES SDPS application.

Burke, John; Ericson, Jon; Mousessian, Ardvas

2007-10-01

399

Eukaryotic Promoter Database  

NSDL National Science Digital Library

The Eukaryotic Promoter Database (EPD), developed at the Weizmann Institute of Science in Israel and currently maintained at the Swiss Institute for Experimental Cancer Research, is an annotated collection of eukaryotic POL II promoters intended to assist experimental researchers as well as computer analysts in the investigation of eukaryotic transcription signals. Promoters are included in EPD if they are recognized by eukaryotic RNA POL II, active in a higher eukaryote, experimentally defined or homologous and sufficiently similar to an experimentally defined promoter, biologically functional, available in the current EMBL release, and distinct from other promoters in the database. Database entries (searchable by organism, homology group, sequence, keywords, references, etc.) include promoter identifications and descriptions, information on the experimental evidence, various kinds of promoter classifications and regulatory properties, as well as bibliographic references and cross-references to other databases. The EPD Website also features yearly-updated base frequency matrices for major eukaryotic promoter elements, a user manual, and a link to a complementary database called EPDX, which allows users to view available gene expression data for human EPD promoters.

1969-12-31

400

ADANS database specification  

SciTech Connect

The purpose of the Air Mobility Command (AMC) Deployment Analysis System (ADANS) Database Specification (DS) is to describe the database organization and storage allocation and to provide the detailed data model of the physical design and information necessary for the construction of the parts of the database (e.g., tables, indexes, rules, defaults). The DS includes entity relationship diagrams, table and field definitions, reports on other database objects, and a description of the ADANS data dictionary. ADANS is the automated system used by Headquarters AMC and the Tanker Airlift Control Center (TACC) for airlift planning and scheduling of peacetime and contingency operations as well as for deliberate planning. ADANS also supports planning and scheduling of Air Refueling Events by the TACC and the unit-level tanker schedulers. ADANS receives input in the form of movement requirements and air refueling requests. It provides a suite of tools for planners to manipulate these requirements/requests against mobility assets and to develop, analyze, and distribute schedules. Analysis tools are provided for assessing the products of the scheduling subsystems, and editing capabilities support the refinement of schedules. A reporting capability provides formatted screen, print, and/or file outputs of various standard reports. An interface subsystem handles message traffic to and from external systems. The database is an integral part of the functionality summarized above.

NONE

1997-01-16

401

Keeping Public Information Public.  

ERIC Educational Resources Information Center

|Discusses the trend toward the transfer of federal government information from the public domain to the private sector. Topics include free access, privatization, information-policy revision, accountability, copyright issues, costs, pricing, and market needs versus public needs. (LRW)|

Kelley, Wayne P.

1998-01-01

402

PMRD: plant microRNA database  

PubMed Central

MicroRNAs (miRNA) are ?21 nucleotide-long non-coding small RNAs, which function as post-transcriptional regulators in eukaryotes. miRNAs play essential roles in regulating plant growth and development. In recent years, research into the mechanism and consequences of miRNA action has made great progress. With whole genome sequence available in such plants as Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Glycine max, etc., it is desirable to develop a plant miRNA database through the integration of large amounts of information about publicly deposited miRNA data. The plant miRNA database (PMRD) integrates available plant miRNA data deposited in public databases, gleaned from the recent literature, and data generated in-house. This database contains sequence information, secondary structure, target genes, expression profiles and a genome browser. In total, there are 8433 miRNAs collected from 121 plant species in PMRD, including model plants and major crops such as Arabidopsis, rice, wheat, soybean, maize, sorghum, barley, etc. For Arabidopsis, rice, poplar, soybean, cotton, medicago and maize, we included the possible target genes for each miRNA with a predicted interaction site in the database. Furthermore, we provided miRNA expression profiles in the PMRD, including our local rice oxidative stress related microarray data (LC Sciences miRPlants_10.1) and the recently published microarray data for poplar, Arabidopsis, tomato, maize and rice. The PMRD database was constructed by open source technology utilizing a user-friendly web interface, and multiple search tools. The PMRD is freely available at http://bioinformatics.cau.edu.cn/PMRD. We expect PMRD to be a useful tool for scientists in the miRNA field in order to study the function of miRNAs and their target genes, especially in model plants and major crops.

Zhang, Zhenhai; Yu, Jingyin; Li, Daofeng; Zhang, Zuyong; Liu, Fengxia; Zhou, Xin; Wang, Tao; Ling, Yi; Su, Zhen

2010-01-01

403

Mandatory public reporting  

Microsoft Academic Search

Purpose – The purpose of this paper is to discuss early experience with American state laws that are starting to mandate public disclosure of adverse outcome event rates from surveillance programs which previously were regarded as a solely confidential activity of internal quality review committees. Design\\/methodology\\/approach – The paper is a literature review of sources identified from the PARADIGM database.

David Birnbaum

2008-01-01

404

Protein structure databases.  

PubMed

Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds-particularly useful for newly solved structures, and especially those of unknown function. Beyond these there are a vast number of databases for the most specialized user, dealing with specific families, diseases, structural features and so on. PMID:21225378

Laskowski, Roman A

2011-06-01

405

Protein structure databases.  

PubMed

Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses, and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds--particularly useful for newly solved structures, and especially those of unknown function. Beyond these there are a vast number of databases for the more specialized user, dealing with specific families, diseases, structural features, and so on. PMID:20221913

Laskowski, Roman A

2010-01-01

406

Scottish Emigration Database  

NSDL National Science Digital Library

Scotland has given the world a great many things, and during the 19th century, many Scots set sail to seek their fortune in other parts of the world. Social historians and others will be glad to know that the University of Aberdeen's Centre for Irish and Scottish Studies has created this online database of Scottish emigrants. Currently, visitors can examine the records of over 21,000 passengers who embarked at Glasgow and Greenock for other ports. While the database only covers a small time period, the database is well-designed for general use. First-time visitors should take a look at the "User Guide", which includes details about the different fields used in each record, such as "occupation", "urban district/village", and "destination port".

407

SODA: Solar Radiation Database  

NSDL National Science Digital Library

The Solar Database, or SoDa, is described as an integration and exploitation of networked Solar radiation Databases for environment monitoring and as a project that aims to integrate European-wide solar radiation resources (i.e. databases, processing chains and educational resources) into one, thematically organized, Web site. The search tool allows users to search for data from a variety of sources including Long Term Time Series Data, Climatological Data, Simulation of Radiation Under Clear Skies Data, Solar Energy Systems Data, and much more. Once a particular set is located, the user can view a description of the source and contents of the data, as well as click on the provided links to access them.

408

Superconductivity Papers Database  

NSDL National Science Digital Library

The Electrotechnical Laboratory (Ministry of International Trade and Industry) and the International Superconductivity Technology Center Foundation (Japan) provide this no-frills, searchable-only bibliographic database of 32,000 superconductivity papers in the areas of High Tc, C60 (Fullerene) related, organic, non-oxide, and oxide conductor. Papers can be searched on title, author, abstract word, or year. The database contains citations mostly from 1987-present in pertinent scholarly journals. The "How to Search" section gives hints on browsing parts of the database via use of the truncation symbol in combination with a classificatory serial number prefix. While there is nothing pretty or particularly user-friendly about the interface, the number of citations on these highly specialized topics should be of use researchers in the field.

1998-01-01

409

FAOSTAT: FAO Statistical Databases  

NSDL National Science Digital Library

In 1997 the Food and Agriculture Organization (FAO) of the United Nations made available several searchable databases containing extensive agricultural data from many countries. Data is provided for production, trade, commodity supply and demand balances, population, land use, and fisheries. Users can select geographical areas, commodities or products, variables relating to those commodities or products, and an annual time series ranging from as early as 1961, depending on the series. Results can be downloaded as text tables, bar or line graphs with user definable axes, or CSV file format -- text with comma separated values for easy import into spreadsheet or other statistical applications. It is important to carefully read the help files that accompany each database in order to fully exploit the searching system. The FAOSTAT Databases give the user access to an amazing amount of country data.

1997-01-01

410

Alcohol Studies Database  

NSDL National Science Digital Library

This database contains citations of over 55,000 documents indexed by the Rutgers University Center of Alcohol Studies since 1987. The database focuses on scholarly and professional materials on beverage alcohol, its use, and related consequences. A small amount of educational and prevention materials and information on other drugs are also included. Visitors may browse by subject headings or search by title or author. Returns include title, author, publisher, year, and page total. Detailed reports also offer a list of related subject headings.

411

Botanical Image Database  

NSDL National Science Digital Library

This database, published by the University of Basel, Switzerland, archives thousands of images (photos and woodcuts) of plants. The collection is arranged alphabetically by species, genus, family, or order, and can be searched by keyword. The advanced search allows users to specify taxonomic groups, physical properties of plants (morphology, growth form, ecology, and others), presentation format, and other parameters. There are also specialized collections from certain geographic regions, and collections of specific types (woody plants, vegetation, pollinators). Each image is accompanied by genus and species, family, a brief description, and location information. The database is available in English and German versions.

2001-09-06

412

Chico State Herbarium Database  

NSDL National Science Digital Library

With over 88,000 mounted and dried specimens, the "Biological Sciences Herbarium at California State University, Chico is the most complete repository of plant specimens from northeastern California. The emphasis is on the local flora, and includes a number of rare, threatened, and endangered plant species." Samples in the Herbarium include ferns, conifers, flowering plants, lichens, bryophytes, and slime molds. The Herbarium Database is still adding specimen label information. The Database includes search fields for Genus, Species, and Subspecies. All higher academic institutions are eligible for specimen loans from the Herbarium.

2007-08-28

413

Earth Impact Database  

NSDL National Science Digital Library

This database contains information on confirmed impact structures around the world. A series of interactive maps, one for each continent, shows the locations of impact structures. Users can roll their mouse over the locations to see structure names and click on them to access physical information such as location (latitude and longitude), diameter, age, maps, photos, cross-sections (where available), and a list of references. The database can also be sorted by age, diameter, or name. There is also a list of the principal criteria for determining if a geological feature is an impact structure, an essay on impact cratering on Earth, and a frequently-asked-questions page.

414

Sandia shock compression database  

NASA Astrophysics Data System (ADS)

An authoritative, updatable, and searchable bibliographic database whose topical area is shock compression is currently under development. The database is derived from published scientific articles and reports with current emphasis in the subareas of strength, phase transitions, spall, and stress-volume relations. The content of the cited work is described by keywords which are selected and reviewed by scientific advisors. Keywords are organized to provide major and minor descriptors which summarize the technical content in considerable detail. Details of theoretical and experimental approaches are described and major emphasis is identified. In addition to bibliographic information, abstracts are also included, and a field is provided for figure captions and able headings.

Anderson, C. E.; Wilbeck, J. S.; Hokanson, J. C.; Asay, J. R.; Grady, D. E.; Graham, R. A.; Kipp, M. E.

415

Organic Compounds Database  

NSDL National Science Digital Library

The Colby College Department of Chemistry offers the Organic Compounds Database, which was compiled by Harold Bell of the Virginia Polytechnic Institute. Visitors can search by the compounds melting point, boiling point, index of refraction, molecular weight, formula, absorption wavelength, mass spectral peak, chemical type, and by partial name. Once entered, results are returned with basically the same type of information that can be searched, plus any other critical information. References are provided for the close to 2500 organic compounds included in the database; yet, because the site was last modified in 1995, varying the data may be required to fully authenticate its accuracy.

Bell, Harold M.

2000-01-01

416

Children's Picture Book Database  

NSDL National Science Digital Library

Located at Miami University, the Children's Picture Book Database indexes abstracts of over 4,000 picture books for children. Designed as tool for teachers creating literature-based thematic units for all disciplines, the database is searchable by a set of topical keywords (over 900) organized by discipline or alphabetically, or by a boolean combination search. Entries include title and author, an abstract, and a list of related keywords. Many of the topic listings also provide related links. A well-organized and useful site for preschool to third grade teachers, parents, and librarians.

417

NBER Macrohistory Database  

NSDL National Science Digital Library

The National Bureau of Economic Research (NBER) (discussed in the September 22, 1995 Scout Report) offers a Macrohistory Database of 3500 monthly, quarterly, and annual economic time series on pre-WWI and interwar economies in addition to their other historical data sets and working papers. Fifteen Macrohistory chapters cover United States production, construction, employment, money, prices, asset market transactions, foreign trade, and government activity, with some coverage of the United Kingdom, France, and Germany. Although the database is searchable by keyword, an analytical index (.pdf format) created by the original NBER compilers gives more detailed information on data series creation and organization.

1998-01-01

418

Databases in Crystal Engineering  

NASA Astrophysics Data System (ADS)

Crystallographic databases are a growing gold mine in the field of crystal engineering (CE), since they contain information precious in many aspects for solid state chemistry. In this contribution we will first enumerate and briefly describe the most relevant crystallographic databases (DB); then we will illustrate some problems that can be addressed by an educated use of DB; in this context we will present examples of remarkable results obtained with the aid of DB. A section will be devoted to the introductory illustration of statistical methods involved in expert use of DB. Knowledge-based applications will be also outlined.

Bacchi, Alessia

419

The California PATH Database  

NSDL National Science Digital Library

The well known Berkeley Digital Library SunSite, discussed in the February 9, 1996 Scout Report, has recently added a new resource to its collection. The PATH database, maintained by the Harmer E. Davis Transportation Library at the University of California, is "the world's largest bibliographical database pertaining to Intelligent Transportation Systems (ITS)." It is searchable and browsable (Browse by ITS Thesaurus Term), and contains over 9,000 records and abstracts "including monographs, journal articles, conference papers, technical reports, theses and selected media coverage," dating back to the 1940s.

1997-01-01

420

Release of ToxCastDB and ExpoCastDB databases  

EPA Science Inventory

EPA has released two databases - the Toxicity Forecaster database (ToxCastDB) and a database of chemical exposure studies (ExpoCastDB) - that scientists and the public can use to access chemical toxicity and exposure data. ToxCastDB users can search and download data from over 50...

421

A Study of the Impact of Statewide Database Licensing on Information Provision in Washington State  

Microsoft Academic Search

The Statewide Database Licensing (SDL) Project brought ProQuest, full-text periodicals and newspapers databases from Bell & Howell, to nearly every library in Washington State. The research presented here investigates the impact of statewide database licensing on the users of public, school and community college libraries. The study was conducted in two stages. At first, transaction log data from Bell &

Efthimis N. Efthimiadis; Harry Bruce

422

The Mouse Genome Database (MGD): expanding genetic and genomic resources for the laboratory mouse  

Microsoft Academic Search

The Mouse Genome Database (MGD) is a comprehen- sive public database of mouse genomic, genetic and phenotypic information (http:\\/\\/www.informatics.jax.org ). This community database provides information about genes, serves as a mapping resource of the mouse genome, details mammalian orthologs, integrates experimental data, represents standardized mouse nomenclature for genes and alleles, incorporates links to other genomic resources such as sequence data,

Judith A. Blake; Janan T. Eppig; Joel E. Richardson; Muriel T. Davisson

2000-01-01

423

Scientific Communication of Geochemical Data and the Use of Computer Databases.  

ERIC Educational Resources Information Center

|Describes a scheme in the United Kingdom that coordinates geochemistry publications with a computerized geochemistry database. The database comprises not only data published in the journals but also the remainder of the pertinent data set. The discussion covers the database design; collection, storage and retrieval of data; and plans for future…

Le Bas, M. J.; Durham, J.

1989-01-01

424

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database  

Microsoft Academic Search

HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics. med.umich.edu\\/hupo\\/ppp; www.ebi.ac.uk\\/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups

Marcin Adamski; Rajasree Menon; Henning Hermjakob; Rolf Apweiler; Arie Admon; Ruedi Aebersold; Helmut Meyer; Young-Ki Paik; Jong-Shin Yoo; Peipei Ping; Joel G. Pounds; Joshua N. Adkins; Xiaohong Qian; Valerie Wasinger; Chi Yue Wu; Xiaohang Zhao; Rong Zeng; Alexander Archakov; Akira Tsugita; Ilan Beer; Akhilesh Pandey; Michael Pisano; Philip Andrews; Harald Tammen

2005-01-01

425

Biological Databases—Insights and Trends  

Microsoft Academic Search

Recent years have seen an explosive growth in biological data, which, instead of being published conventionally, is instead\\u000a deposited in a database (for the number and size of completely sequenced genomes see Figure 1). Sequence data from mega-sequencing\\u000a projects may not even be linked to a conventional publication. This trend and the need for computational analyses of the data\\u000a have

Manuela Pruess

426

Development of a bird banding recapture database  

USGS Publications Warehouse

Recaptures (and resightings) constitute the vast majority of post-release data from banded or otherwise marked nongame birds. A powerful suite of contemporary analytical models is available for using recapture data to estimate population size, survival rates and other parameters, and many banders collect recapture data for their project specific needs. However, despite widely recognized, broader programmatic needs for more and better data, banders' recapture data are not centrally reposited and made available for use by others. To address this need, the US Bird Banding Laboratory, the Canadian Bird Banding Office and the Georgia Cooperative Fish and Wildlife Research Unit are developing a bird banding recapture database. In this poster we discuss the critical steps in developing the database, including: determining exactly which recapture data should be included; developing a standard record format and structure for the database; developing electronic means for collecting, vetting and disseminating the data; and most importantly, developing metadata descriptions and individual data set profiles to facilitate the user's selection of appropriate analytical models. We provide examples of individual data sets to be included in the database, and we assess the feasibility of developing a prescribed program for obtaining recapture data from banders who do not presently collect them. It is expected that the recapture database eventually will contain millions of records made available publicly for a variety of avian research and management purposes

Tautin, J.; Doherty, P.F., Jr.; Metras, L.

2001-01-01

427

BAX: an X-ray cluster database  

NASA Astrophysics Data System (ADS)

X-ray observations of clusters of galaxies have matured rapidly in the last years with the advent of good quality imaging and spectroscopy. All these observations added to those gathered since early 70's resulted in large amount of X-ray data for thousands groups and clusters of galaxies published in a rapidly increasing number of papers. It is becoming clear that the ever increasing amount of scientific X-ray high quality data and publications require a dedicated database. By now, there exist no X-rays clusters dedicated database as it exist for the stellar ( CDS ) and extragalactic objects ( e.g. NED, LEDA). We present BAX, a database for X-rays clusters of galaxies information retrieval available on the web. BAX will provide the user with basic data published in the literature and the bibliography related to X-rays clusters of galaxies. The structure of BAX differs from existing databases such as NED, SIMBAD, VIZIER or LEDA and is the first database compiling information on clusters of galaxies.

Sadat, R.; Blanchard, A.

428

Rational Design of Human DNA Ligase Inhibitors that Target Cellular DNA Replication and Repair  

Microsoft Academic Search

Based on the crystal structure of human DNA ligase I complexed with nicked DNA, computer-aided drug design was used to identify compounds in a database of 1.5 million commercially available low molecular weight chemicals that were predicted to bind to a DNA-binding pocket within the DNA-binding domain of DNA ligase I, thereby inhibiting DNA joining. Ten of 192 candidates specifically

Xi Chen; Shijun Zhong; Xiao Zhu; Barbara Dziegielewska; Tom Ellenberger; Gerald M. Wilson; Alexander D. MacKerell; Alan E. Tomkinson

2008-01-01

429

WHITHER BIOLOGICAL DATABASE RESEARCH?  

Technology Transfer Automated Retrieval System (TEKTRAN)

We consider how the landscape of biological databases may evolve in the future, and what research is needed to realize this evolution. We suggest today's dispersal of diverse resources will only increase as the number and size of those resources, driving the need for semantic interoperability even ...

430

Creating an Experts Database.  

ERIC Educational Resources Information Center

|Many organizations are creating a database of technical experts as a mechanism for identifying key people who can solve problems, transfer information and best practices, and/or identify other experts with the needed expertise. This article discusses experts versus skills; identifying experts; responsibilities of the expert; expert profiles;…

Hodgson, Cynthia A.

1999-01-01

431

ENVIRONMENTAL FATE DATABASE (ENVIROFATE)  

EPA Science Inventory

The Environmental Fate Database contains more than 13,000 records of information on the environmental fate or behavior (i.e., transport and degradation) of approximately 800 chemical released into the environment. Chemicals selected for inclusion are produced in quantities exceed...

432

The Fingerprinted Database  

Microsoft Academic Search

A fingerprinting database management system presents a unique version or view of the data to each user. The view contains small pseudorandom modifications to selected data items. The objective of this system is to identify users who divulge proprietary information which they have obtained through legitimate access. Even if the user makes further modifications to the data before its misuse,

Neal R. Wagner; Robert L. Fountain; Robert J. Hazy

1990-01-01

433

LHCb distributed conditions database  

NASA Astrophysics Data System (ADS)

The LHCb Conditions Database project provides the necessary tools to handle non-event time-varying data. The main users of conditions are reconstruction and analysis processes, which are running on the Grid. To allow efficient access to the data, we need to use a synchronized replica of the content of the database located at the same site as the event data file, i.e. the LHCb Tier1. The replica to be accessed is selected from information stored on LFC (LCG File Catalog) and managed with the interface provided by the LCG developed library CORAL. The plan to limit the submission of jobs to those sites where the required conditions are available will also be presented. LHCb applications are using the Conditions Database framework on a production basis since March 2007. We have been able to collect statistics on the performance and effectiveness of both the LCG library COOL (the library providing conditions handling functionalities) and the distribution framework itself. Stress tests on the CNAF hosted replica of the Conditions Database have been performed and the results will be summarized here.

Clemencic, M.

2008-07-01

434

Patent Family Databases.  

ERIC Educational Resources Information Center

|Reports on retrieval of patent information online and includes definition of patent family, basic and equivalent patents, "parents and children" applications, designated states, patent family databases--International Patent Documentation Center, World Patents Index, APIPAT (American Petroleum Institute), CLAIMS (IFI/Plenum). A table noting…

Simmons, Edlyn S.

1985-01-01

435

WETLANDS TREATMENT DATABASE  

EPA Science Inventory

The U.S. EPA sponsored a project to collect and catalog information from wastewater treatment wetlands into a computer database. PA has also written a user friendly, stand-alone, menu-driven computer program to allow anyone with DOS 3.3 or higher to access the information in the ...

436

Database for Propagation Models.  

National Technical Information Service (NTIS)

A database of various propagation phenomena models that can be used by telecommunications systems engineers to obtain parameter values for systems design is presented. This is an easy-to-use tool and is currently available for either a PC using Excel soft...

A. V. Kantak K. Suwitra C. Le

1994-01-01

437

Weathering Database Technology  

ERIC Educational Resources Information Center

Collecting weather data is a traditional part of a meteorology unit at the middle level. However, making connections between the data and weather conditions can be a challenge. One way to make these connections clearer is to enter the data into a database. This allows students to quickly compare different fields of data and recognize which…

Snyder, Robert

2005-01-01

438

ECOREGION SPATIAL DATABASE  

EPA Science Inventory

This spatial database contains boundaries and attributes describing Level III ecoregions in EPA Region 8. The ecoregions shown here have been derived from Omernik (1987) and from refinements of Omernik's framework that have been made for other projects. These ongoing or re...

439

Mutating database queries  

Microsoft Academic Search

A set of mutation operators for SQL queries that retrieve information from a database is developed and tested against a set of queries drawn from the NIST SQL Conformance Test Suite. The mutation operators cover a wide spectrum of SQL features, including the handling of null values. Additional experiments are performed to explore whether the cost of executin g mutants

Javier Tuya; María José Suárez Cabal; Claudio De La Riva

2007-01-01

440

Aging Aircraft Structures Database.  

National Technical Information Service (NTIS)

This report summarizes the work performed by the Boeing Company to develop an aging aircraft structures database to be used to aid in the verification of structural integrity analysis of aircraft structures. Sample data were collected for the C-30 EC-135,...

R. Perez

1998-01-01

441

ISDB: Interaction Sentence Database  

Microsoft Academic Search

BACKGROUND: Rapid growth in the scientific literature available on-line continues to motivate shifting data analysis from humans to computers. For example, greater knowledge of sentence characteristics indicative of interaction between two biological entities is needed to aid in the creation of better-performing information extraction tools for effectively using this rich body of information. FINDINGS: The Interaction Sentence Database (ISDB) allows

Michael A Bauer; Robert E Belford; Jing Ding; Daniel Berleant

2010-01-01

442

A multilingual prosodic database  

Microsoft Academic Search

We present a prosodic corpus in five languages (French, English, Italian, German and Spanish) comprising 4 hours and 20 minutes of speech and involving 50 different speakers (5 male and 5 female per language). The recordings on which the corpus is based are extracted from the EUROM 1 speech database and consists of passages of about five sentences. The corpus

Estelle Campione; Jean Véronis

1998-01-01

443

NATIONAL ASSESSMENT DATABASE (NAD)  

EPA Science Inventory

Resource Purpose: The National Assessment Database stores State water quality assessments that are reported under Section 305(b) of the Clean Water Act. The data are stored by individual water quality assessments. Threatened, partially and not supporting waters also have da...

444

Rethinking integrity [distributed databases  

Microsoft Academic Search

In practice, no real database enjoys complete integrity, a variety of factors conspire to make some information stale, missing, or just plain wrong. System design and analysis should recognize that real systems lack integrity to some degree, most, if not all, of the time. Significant benefits flow from such recognition. Risk management techniques can identify the severity of different integrity-loss

Paul Ammann; S. Jajodia

1997-01-01

445

SGD: Saccharomyces Genome Database  

Microsoft Academic Search

The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic s equence, i ts g enes a nd t heir products, the p henotypes of i ts m utants, a nd t he literature supporting these data. The amount of information and t he n umber o f features p rovided b y SGD have i

J. Michael Cherry; Caroline Adler; Catherine A. Ball; Stephen A. Chervitz; Selina S. Dwight; Erich T. Hester; Yankai Jia; Gail Juvik; Taiyun Roe; Mark Schroeder; Shuai Weng; David Botstein

1998-01-01

446

GENERAL PERMITS DATABASE  

EPA Science Inventory

Resource Purpose: This database was used to provide permit writers with a library of examples for writing general permits. It has not been maintained and is outdated and will be removed. Water Permits Division is trying to determine whether or not to recreate this databas...

447

PESTICIDE USE REPORT DATABASE  

EPA Science Inventory

This dataset summarizes pesticide use in California for year 1990-96 as extracted from the Pesticide Use Report (PUR) by county. The PUR is a comprehensive database of Pesticide Use in the state of California supplied by the DPR (California Department of Pesticide Regulation). ...

448

Updating the DXplain Database  

PubMed Central

DXplain is a computer-based medical information system designed to accept a patient's historical, physical, and laboratory findings and then generate a list of diseases which could explain some or all of the data. This paper describes recent updating of the database with special attention to the software techniques used increasingly to facilitate the process.

Packer, Marvin S.; Cimino, James J.; Hoffer, Edward P.; Barnett, G. Octo; Kim, Richard; Zatz, Stephen

1988-01-01

449

PADB : Published Association Database  

Microsoft Academic Search

BACKGROUND: Although molecular pathway information and the International HapMap Project data can help biomedical researchers to investigate the aetiology of complex diseases more effectively, such information is missing or insufficient in current genetic association databases. In addition, only a few of the environmental risk factors are included as gene-environment interactions, and the risk measures of associations are not indexed in

Hwanseok Rhee; Jin-sung Lee

2007-01-01

450

The CEBAF Element Database  

SciTech Connect

With the inauguration of the CEBAF Element Database (CED) in Fall 2010, Jefferson Lab computer scientists have taken a step toward the eventual goal of a model-driven accelerator. Once fully populated, the database will be the primary repository of information used for everything from generating lattice decks to booting control computers to building controls screens. A requirement influencing the CED design is that it provide access to not only present, but also future and past configurations of the accelerator. To accomplish this, an introspective database schema was designed that allows new elements, types, and properties to be defined on-the-fly with no changes to table structure. Used in conjunction with Oracle Workspace Manager, it allows users to query data from any time in the database history with the same tools used to query the present configuration. Users can also check-out workspaces to use as staging areas for upcoming machine configurations. All Access to the CED is through a well-documented Application Programming Interface (API) that is translated automatically from original C++ source code into native libraries for scripting languages such as perl, php, and TCL making access to the CED easy and ubiquitous.

Theodore Larrieu, Christopher Slominski, Michele Joyce

2011-03-01

451

CRREL Ice Jam Database.  

National Technical Information Service (NTIS)

This report provides information on the CRREL Ice Jam Database and its potential use for analyzing ice-related flooding problems. Rivers in the northern United States are subject to ice jams that cause flooding; block hydropower and water supply intakes; ...

K. D. White H. J. Eames

1999-01-01

452

Database Technologies for RDF  

NASA Astrophysics Data System (ADS)

Efficient and scalable support for RDF/OWL data storage, loading, inferencing and querying, in conjunction with already available support for enterprise level data and operations reliability requirements, can make databases suitable to act as enterprise-level RDF/OWL repository and hence become a viable platform for building semantic applications for the enterprise environments.

Das, Souripriya; Srinivasan, Jagannathan

453

The Indra Simulation Database  

NASA Astrophysics Data System (ADS)

We present the Indra suite of cosmological N-body simulations and the design of its companion database. Indra consists of 512 different instances of a 1 Gpc/h-sided box, each with 100 million dark matter particles and the same input cosmology, enabling a characterization of very large-scale modes of the matter power spectrum with galaxy-scale mass resolution and an excellent handle on cosmic variance. Each simulation outputs 64 snapshots, giving over 100 TB of data for the full set of simulations, all of which will be loaded into a SQL database. We discuss the database design for the particle data, consisting of the positions and velocities of each particle; the FOF halos, with links to the particle data so that halo properties can be calculated within the database; and the density field on a power-of-two grid, which can be easily linked to each particle's Peano-Hilbert index. Initial performance tests and example queries will be given. The authors are grateful for support from the Gordon and Betty Moore and the W.M. Keck Foundations.

Falck, Bridget; Budavari, T.; Cole, S.; Crankshaw, D.; Dobos, L.; Lemson, G.; Neyrinck, M.; Szalay, A.; Wang, J.

2011-05-01

454

Enzyme Database - BRENDA  

NSDL National Science Digital Library

BRENDA is the main collection of enzyme functional data available to the scientific community. It is available free of charge for via the internet (www.brenda-enzymes.info) and as an in-house database for commercial users (requests to our distributor Biobase).

Institute Of Biochemistry And Bioinformatics At The Technical University Of Braunschweig, Germany

455

Trace Fossil Image Database  

NSDL National Science Digital Library

This database from Emory University consists of images and basic information concerning trace fossils photographed by Anthony Martin. Included in this information is the formation, age, and locality of the specimen if known. Many of the images were originally photographed while in the field, and each type of trace fossil has numerous examples to browse through.

Martin, Anthony; University, Emory

456

Physical Database Design Techniques  

Microsoft Academic Search

The physical database design problem has received considerable attention in the past. In this paper we present a sample of the techniques and models used to solve some of the problems in this area. A detailed analysis of two of these problems is shown.

Mario Schkolnick

1979-01-01

457

Metadata in video databases  

Microsoft Academic Search

Video is composed of audio-visual information. Providing content based access to video data is essential for the sucessful integration of video into computers. Organizing video for content based access requires the use of video metadata. This paper explores the nature video metadata. A data model for video databases is presented based on a study of the applications of video, the

Ramesh Jain; Arun Hampapur

1994-01-01

458

Mars Observer Database.  

National Technical Information Service (NTIS)

Mars Observer will study the surface, atmosphere, and climate of Mars in a systematic way over an entire Martian year. The observations of the surface will provide a database that will be invaluable to the planning of a future Mars sample return mission. ...

A. L. Albee

1988-01-01

459

Visual Palaeomagnetic Database  

NASA Astrophysics Data System (ADS)

The Global Palaeomagnetic Database (GPMDB) created and developed by McElhinny and Lock (1991, 1996) is used by researchers all over the world. The user-friendly interface makes it unnecessary for users to learn about details of the Microsoft Access software. The next step in the development of these databases lies in the visualisation of data and in the integration of the palaeomagnetic data with Geographical Information Systems (GIS). One of the most popular GIS software among Earth scientists is ArcView. Due to the relative simplicity of the structure of the GPMDB it quite easy to integrate palaeomagnetic data into GIS. It is just necessary to prepare a database file in DBASE format (using the export option of the Microsoft Access, for example) and then to create a subsequent graphic theme (layer) in ArcView. The wide variety of ArcView options enable the use of graduated colours, labels, and different symbols to emphasise ages, palaeomagnetic directions, or other data features. Palaeomagnetic data may be combined with the geological, tectonic, and other maps using a variety of spherical projections. Palaeomagnetic data may be easily integrated into other GIS-oriented databases, such as geochronological databases. In addition to all "traditional" services known for the GPMDB users, such as queries, ArcView and supplementary Avenue scripts provide many new possibilities. For example, it is very easy now to choose data from a particular polygon (e.g. craton, terrane, orogenic belt etc.). Users of the new visual database also can "instantly" create a stereoplot for any selected data subset and to calculate mean directions and palaeopoles. It is also possible to display palaeopoles for the selected group of data and to reconstruct a palaeoposition of the continental block using these poles, or Euler pole of rotation. There are obvious advantages of using the visual database. For example, if there are some errors in the geographical position of some data, in many cases it is easy to find them. It is much easier now to test tectonic hypotheses. For instance, it is possible to compare data from two adjacent terranes to decide the time of their collision.

Pisarevsky, S.

2002-12-01

460

DNA Sequencing apparatus  

DOEpatents

An automated DNA sequencing apparatus having a reactor for providing at least two series of DNA products formed from a single primer and a DNA strand, each DNA product of a series differing in molecular weight and having a chain terminating agent at one end; separating means for separating the DNA products to form a series bands, the intensity of substantially all nearby bands in a different series being different, band reading means for determining the position an This invention was made with government support including a grant from the U.S. Public Health Service, contract number AI-06045. The U.S. government has certain rights in the invention.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

1992-01-01

461

Publishing Your Database on CD-ROM for Profit: The FISHLIT and NISC Experience.  

ERIC Educational Resources Information Center

|Details the development of the FISHLIT bibliographic database at the JLB Smith Institute of Ichthyology Library at Rhodes University (South Africa), and the subsequent CD-ROM publication of the database by NISC (National Information Services Corporation). Discusses the advantages of CD-ROM publication, costs and information service provision,…

Crampton, Margaret

1995-01-01

462

Publishing Your Database on CD-ROM for Profit: The FISHLIT and NISC Experience.  

ERIC Educational Resources Information Center

Details the development of the FISHLIT bibliographic database at the JLB Smith Institute of Ichthyology Library at Rhodes University (South Africa), and the subsequent CD-ROM publication of the database by NISC (National Information Services Corporation). Discusses the advantages of CD-ROM publication, costs and information service provision,…

Crampton, Margaret

1995-01-01

463

MEROPS: the peptidase database.  

PubMed

The MEROPS database (http://www.bi.bbsrc.ac.uk/Merops/Merops.+ ++htm) provides a catalogue and structure-based classification of peptidases (i.e. all proteolytic enzymes). This is a large group of proteins (approximately 2% of all gene products) that is of particular importance in medicine and biotechnology. An index of the peptidases by name or synonym gives access to a set of files termed PepCards each of which provides information on a single peptidase. Each card file contains information on classification and nomenclature, and hypertext links to the relevant entries in online databases for human genetics, protein and nucleic acid sequence data and tertiary structure. Another index provides access to the PepCards by organism name so that the user can retrieve all known peptidases from a particular species. The peptidases are classified into families on the basis of statistically significant similarities between the protein sequences in the part termed the 'peptidase unit' that is most directly responsible for activity. Families that are thought to have common evolutionary origins and are known or expected to have similar tertiary folds are grouped into clans. The MEROPS database provides sets of files called FamCards and ClanCards describing the individual families and clans. Each FamCard document provides links to other databases for sequence motifs and secondary and tertiary structures, and shows the distribution of the family across the major kingdoms of living creatures. Release 3.03 of MEROPS contains 758 peptidases, 153 families and 22 clans. We suggest that the MEROPS database provides a model for a way in which a system of classification for a functional group of proteins can be developed and used as an organizational framework around which to assemble a variety of related information. PMID:9847218

Rawlings, N D; Barrett, A J

1999-01-01

464

Mathematical methods for DNA sequences  

SciTech Connect

This book contains the procedure on mathematical methods for DNA sequences. Topics covered include: Development of database for nucleotide sequences, Analysis with restriction enzymes, Sequence alignments Consensus patterns in sequences, Some statistical aspects of the primary structure of nucleotide sequences, Patterns in DNA and amino acid sequences and their statistical significance.

Waterman, M.S. (Mathematics and Molecular Biology, Univ. of Southern California, Los Angeles, CA (US))

1989-01-01

465

5S ribosomal RNA database Y2K  

Microsoft Academic Search

This paper presents the updated version (Y2K) of the database of ribosomal 5S ribonucleic acids (5S rRNA) and their genes (5S rDNA), http:\\/\\/rose.man\\/poznan. pl\\/5SData\\/index.html . This edition of the database contains 1985 primary structures of 5S rRNA and 5S rDNA. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S

Maciej Szymanski; Miroslawa Z. Barciszewska; Jan Barciszewski; Volker A. Erdmann

2000-01-01

466

cDNA cloning, overproduction and characterization of rat adrenodoxin reductase 1 1 The nucleotide sequence data reported in this paper will appear in the GSDB, DDBJ, EMBL and NCBI nucleotide sequence databases with accession number D63761  

Microsoft Academic Search

We isolated a full-length cDNA clone for rat adrenodoxin reductase (AdR). The precursor of rat AdR was predicted to consist of 34 amino-terminal residues of extrapeptide for transport into mitochondria and the following 460 residues of the mature peptide region. The deduced amino acid sequence was 70.8 and 61.8% homologous to those of bovine and human AdRs in the extrapeptide

Yasuhiro Sagara; Yoshiya Watanabe; Hiroyuki Kodama; Hironori Aramaki

1999-01-01

467

The GLIMS Glacier Database  

NASA Astrophysics Data System (ADS)

The Global Land Ice Measurements from Space (GLIMS) project has built a geospatial and temporal database of glacier data, composed of glacier outlines and various scalar attributes. These data are being derived primarily from satellite imagery, such as from ASTER and Landsat. Each "snapshot" of a glacier is from a specific time, and the database is designed to store multiple snapshots representative of different times. We